FIX formatting of readme headings
FIX formatting of readme headings

Squashed commit of the following:

commit fe2cb5614e6c2b9a686594d80d0efe66e5100572
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Wed Mar 29 18:16:26 2017 +0200

    DEL conservation analysis files

    Squashed commit of the following:

    commit 6e16f644c008fb3ff97766072f50805ba5dbe46e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Mar 29 18:05:54 2017 +0200

        MNT resolve conflicts and bump to 1.1.5

        Conflicts:
        	CHANGELOG.md
        	docs/custom-alignment-files.html
        	docs/installation.html
        	docs/running-example.html
        	docs/usage-instructions.html
        	docs/usage-instructions.md
        	notebooks/rpbp-predictions/create-orf-type-pie-chart.ipynb
        	rpbp/analysis/profile_construction/create_preprocessing_report.py
        	rpbp/analysis/profile_construction/create_read_length_metagene_profile_plot.py
        	rpbp/analysis/profile_construction/get_all_read_filtering_counts.py
        	rpbp/reference_preprocessing/prepare_rpbp_genome.py
        	rpbp/run_all_rpbp_instances.py
        	rpbp/run_rpbp_pipeline.py
        	setup.py

    commit 98d3e645316b437227652c4d61b9347036a5ea9f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Mar 29 17:42:48 2017 +0200

        MNT version bump to 1.1.4

    commit d256a2c58b3b984ffd4045b8989bffe84a1808d8
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Mar 29 17:34:33 2017 +0200

        FIX prepare-rpbp-genome checks that annotation files exist

        This addresses Issue #62.

    commit d3b69f85d71299e942e63073b8dd90c863d148e2
    Merge: 24914cb 9edde5b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Mar 29 17:31:27 2017 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 9edde5b0f6c331236e3adba8ed93ababf2cde0c2
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Mar 3 19:02:53 2017 +0100

        UPD docs for prediction report

        This addresses part of Issue #23

    commit 24914cbaa69e01ff089c45d6bac4a776d5dc6ec3
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Mar 3 17:26:14 2017 +0100

        UPD renamed "replicate_name" to "condition_name"

    commit d086cc0ebbe8ca98b96ba59c842c1727ac6e04ec
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 28 16:24:31 2017 +0100

        FIX removed --tmp from run-rpbp-pipeline for predict-translated-orfs call

    commit e512dbaa21ae660df87fcd3ba87f91b17fbc5509
    Merge: e915d99 ea1648f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 18:38:23 2017 +0100

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit ea1648fb3a8f3f78c6e482bf9ad4a5eed1757bef
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 18:37:52 2017 +0100

        DEL extract-orf-types script

    commit 273393e198ed5134e8a5dea7bc50fa03c5592091
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 18:36:38 2017 +0100

        MNT renamed create-rpbp-preprocessing-report

    commit b1632b26895527fcf25bbdc1f958225715b1e5e6
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 18:33:52 2017 +0100

        UPD docs for visualizing predicted ORF types

        This is a part of Issue #23.

    commit e915d99cde0f80bb00b5b9f8151ba12ae713c6c8
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 18:06:16 2017 +0100

        ADD ipython nbs for visualizing predicted ORF types

    commit bfac4079b20d5a6f56dd056bcea229eeb1d10cee
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 17:45:15 2017 +0100

        ADD create-orf-types-bar-chart for visualizing predicted ORF types

        This also replaces create-orf-types-pie-chart in the predictions report.

    commit a75b56c9594c2b82de6026a2bd87c57c5fd931b9
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 17:44:18 2017 +0100

        MNT renamed create-rpbp-predictions-report

    commit 6effc50c7806575d0dc58b2e64fb75bcc6ff86ea
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 16:41:23 2017 +0100

        DEL conservation analysis scripts

        These scripts looked for significant overlaps with the Mackowiak predictions.
        The results were not very promising, and the scripts were not robust, so I
        removed them.

    commit 94d348fc31341b53cc4fe23862e665c280f2bb55
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 16:03:15 2017 +0100

        UPD docs for preprocessing report

        This is a part of Issue #23.

    commit b611b4e220104e6919097265e11673efbfdeeba5
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 15:20:31 2017 +0100

        DEL unused option from create-read-length-metagene-profile-plot

        The series-label option is no longer used, so it was removed.

    commit 615383db9bf6488ede39b5a4cda8a621d9d91091
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 15:03:12 2017 +0100

        UPD docs for creating read length metagene profiles

        This is related to Issue #23.

    commit b3cdacebefe3dca4575d99bf71a1186f2c015974
    Merge: b3dc587 66295c7
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 14:36:13 2017 +0100

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit b3dc58704b91136f9688448b08e92ccba210597a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 14:35:32 2017 +0100

        DEL references to [analysis] feature

        All of the scripts are now installed.

    commit 66295c7ef8937454a53ba18a7c37989fecd32e3a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 27 14:19:58 2017 +0100

        UPD docs for creating read length distribution

        This commit also includes small updates to how the preprocessing report calls
        the read length distribution creation and visualization scripts.

        This is related to Issue #23.

    commit d7d938c9bbd7d0c0ef55c848ba9e21f9d4d62bcd
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 23 18:31:17 2017 +0100

        MNT merge with 1.1.3 fix to master

        Conflicts:
        	CHANGELOG.md
        	docs/custom-alignment-files.html
        	docs/installation.html
        	docs/running-example.html
        	docs/usage-instructions.html
        	docs/usage-instructions.md
        	rpbp/__init__.py
        	rpbp/analysis/profile_construction/get_all_read_filtering_counts.py
        	rpbp/analysis/profile_construction/visualize_read_filtering_counts.py
        	rpbp/run_all_rpbp_instances.py
        	setup.py

    commit 8a2663c1e958027c3a7cdb1d717987dcb340e00f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 23 18:09:35 2017 +0100

        UPD changes for upcoming version in change log

    commit 583bae1d4e566622b2f29f3e192ab6bb82326c28
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 23 17:25:41 2017 +0100

        ADD makefile for creating html, pdf docs from md

    commit 403972f59c07459963b81b3cee44a3f1741984cf
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 23 17:24:42 2017 +0100

        ADD docs on creating reference indices.

        These are suggestions on where to find appropriate annotations, etc. It does
        repeat (much) information from the usage instructions.

    commit 8a7403f4fe16a45b1229a865588a531f0e27e575
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 22 17:23:05 2017 +0100

        UPD replaced read-filtering paths with generic ones and comments

    commit b9856a98770783623bad4d8bdb98dc3e9427936a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 22 17:18:21 2017 +0100

        FIX added read count image to git

    commit 5860caec774cd00949f17274d39ebccd11b42510
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 22 17:17:05 2017 +0100

        ADD docs for counting and visualizing reads at each filtering step

    commit 11064ac3a6ceb19e943f73c6e935a9417571e644
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 21 18:53:59 2017 +0100

        FIX remove --tmp from call to predict-translated-orfs in main pipeline

    commit e6ef991373edd90b5abc3cd510be9b395ce92a52
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 21 11:54:53 2017 +0100

        ADD documentation for create-read-length-orf-profiles

    commit 4efdde74276577308fe3709df3babc1d768b7118
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 15 17:00:34 2017 +0100

        MNT version bump in setup, __init__ and change log

    commit 95e1a84ce3c3880da541dcb9f8c98c0ceb185c50
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 15 16:55:37 2017 +0100

        FIX star expansion synax in estimate-orf-bayes-factors.

        This addresses the problem at the bottom of Issue #51

    commit 0d3a8c07592c64bbe538dacdc5159d0a797e87dc
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 15 00:31:25 2017 +0100

        Conflicts:
        	.gitignore
        	CHANGELOG.md
        	README.md
        	docs/custom-alignment-files.html
        	docs/custom-alignment-files.md
        	docs/installation.html
        	docs/installation.md
        	docs/running-example.html
        	docs/running-example.md
        	docs/usage-instructions.html
        	docs/usage-instructions.md
        	rpbp/analysis/profile_construction/create_preprocessing_report.py
        	rpbp/analysis/rpbp_predictions/create_predictions_report.py
        	rpbp/process_all_samples.py
        	rpbp/process_all_samples.py.bak
        	rpbp/run_all_rpbp_instances.py
        	setup.py

    commit 68e3d1addecbdf4d549e489da560054d07f4e788
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 17:36:29 2017 +0100

        ADD change log

    commit 1f64a4f224b9bf04c19f2b2a1783a460b4e60691
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 16:44:19 2017 +0100

        MNT removed all references to (py)bedtools

        This addresses Issue #47.

    commit 91b96567b7412bc71133bc194a738c8b30716bc1
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 16:29:41 2017 +0100

        DEL ipython doc notebooks

        These were redundant, and the conversion to markdown does not always work that
        well. pandoc can be used to convert the md files to html for local viewing.

    commit 22d52b869f34e56390fdce3f30c8f0c078b55996
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 16:28:50 2017 +0100

        ADD anaconda installation instructions

        This addresses Issue #46.

    commit 48a9317ca99da9304d47d83eb5f57d92ae65e6cf
    Merge: 08e3d5c 46fb2f4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 15:32:34 2017 +0100

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 08e3d5ceaed1e57206d99d03214b63b08f1fdc90
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 15:28:46 2017 +0100

        UPD docs include (novel) ORF labeling meanings.

        This also updates all of the examples to use the new script names.

        This addresses Issue #48.

    commit 46fb2f44288e819198773ac06aa918713abeb463
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 13:08:05 2017 +0100

        FIX removed "mock" values for length, offset in read-length-specific scripts

    commit 0f964c71481ff4153ac8eb95540dd3196a58048c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Feb 14 11:46:37 2017 +0100

        UPD use config for read-length specific ORF profile files

        This is in relation to Issue #49.

    commit e92aae0d0273fb5554f2eee629602f212ce0584b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 13 17:58:41 2017 +0100

        ADD scripts to create read length-specific ORF profiles

        This addresses Issue #49.

    commit 968221a1e46d909b1d42b27f9a204268ec71b919
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 13 15:45:02 2017 +0100

        UPD progress bar for finding P-site itersections

    commit 86d1649cb75bf92a6c0f5a1611a496df4ae52b7f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 13 15:33:10 2017 +0100

        DEL old script to smooth profiles

    commit 5a5effcd7488d8a226e3478174adede76e124129
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Feb 13 14:11:12 2017 +0100

        FIX pass --mem flag to run-rpbp-pipeline from run-all script.

        This addresses Issue #50.

    commit 5e597c70394466d42405b8d93f2863af36005986
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Feb 10 18:10:09 2017 +0100

        UPD pass memory request to STAR

        This addresses Issue #50.

    commit eb38056917027f3e07739db5f53fe83a49e6bfc0
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 9 10:54:13 2017 +0100

        UPD removed all mentions of gffread from docs

    commit f334b2c82e16119fd92d1a8f9efb40a1b4382681
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 9 10:53:26 2017 +0100

        MNT added citation to readme

    commit a902233e658bfca60bc638bf96af23edd6d74e4e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 9 09:49:02 2017 +0100

        FIX handle references with no 5' leader or 3' trailer regions.

        This addresses Issue #43.

        Additionally, some of the more detailed debug statements which are addressed
        in unit tests have been removed.

    commit 7306e80adab46c42bb11ef1a310e8634ec67af8b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 8 18:51:29 2017 +0100

        RM old translated model files.

        This is related to a discussion at the end of Issue #44.

    commit 8ad57332feeb562403278a1c3e837780961b169a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 8 11:06:32 2017 +0100

        FIX "private" dependencies are handled with requirements.txt.

        This addresses Issue #44.

    commit 519397530a70a1137284992834495110bd33b2dd
    Merge: 0861a5d 7337149
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Feb 4 00:40:41 2017 +0100

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 0861a5d7bd3b24241b937ca70f8b6848aa1a4482
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Feb 4 00:39:36 2017 +0100

        FIX readFilesCommand for star can be user-specified.

        This addresses Issue #35

    commit 7337149456a7853d09b7e61efa790a79b44175d7
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Feb 3 18:28:52 2017 +0100

        FIX handle no periodic read lengths in get-all-read-filtering-counts

    commit cac863659680cf21f9d138ab8565ef69bf998210
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 2 18:51:29 2017 +0100

        UPD metagene profile image ranges in preprocessing report

        This addresses Issue #38

    commit 871182dd11aeddd64f04471fb11a49aa1bec2e05
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 2 13:59:25 2017 +0100

        UPD put read length distributions in table for preprocessing report

        This addresses Issue #37

    commit 0e5e47cbe3da64af2c5af8e2e2d59b4557fac2f9
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 2 13:27:39 2017 +0100

        UPD orf type periodicity is optional in reporting

        This includes both the preprocessing and predictions report. It addresses
        Issue #39.

    commit 5c0bf21a25d3d144a36849d9ab3d47cac8b199e7
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Feb 2 11:49:03 2017 +0100

        ADD option to skip unfiltered ORFs in prediction report

        This addresses Issue #40

    commit f85be17bd59b4a4ad61b6221d5cae4b1c79ff5e5
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 20:08:48 2017 +0100

        UPD split p-sites in extract-orf-profiles based on exons.

        This does not appear to actually reduce memory overhead because of the way
        joblib handles forking the python process. It does still avoid unnecessarily
        looking at p-sites, though, so it can stay.

    commit 1abf115f373ea99e0a29f440eb8427da2df8ac04
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 20:07:58 2017 +0100

        FIX use agg backend for filtered read count bar charts

    commit 3231c4f3a1c45dae669c562bcbe9d343e48c5322
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 17:24:16 2017 +0100

        UPD seaborn dependency

    commit dacf30febca4a35d5cefe1ee9e8dad8e8d45b527
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 17:19:05 2017 +0100

        FIX title for read filtering bar chart

    commit b11badd49155a0e46afa906fcb8c0d5c264ca537
    Merge: 07e18bd 158c386
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 17:15:07 2017 +0100

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 07e18bdab0ad0894b689b4d52aa96e2dc4ff168e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 17:14:24 2017 +0100

        UPD read filtering bar charts to use seaborn, mpl_utils

    commit 158c386225d47d5f57866c571566b8cb20f13adc
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 09:17:04 2017 +0100

        FIX slurm-handling in extract-orf-profiles

    commit 1c4ac7bb99770812d57f922684b70a5712ab87af
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 1 09:12:18 2017 +0100

        UPD slurm, input checking for extract-orf-profiles

    commit fb69b510f060b131d1e56a4fe42f98bb801699bd
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Nov 16 19:40:25 2016 +0100

        ADD docs for using custom alignment files

        This commit also includes other small changes to other documentation files.

    commit d6bd8b8fdbb98aacd22112ef82d0cecf37d52184
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Nov 16 19:01:07 2016 +0100

        FIX reference files to be consistent with ribo-te

    commit 1e12fae9aaaf9d3d7b021c17e692221f74d6a419
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Nov 13 20:46:58 2016 +0100

        FIX concat orfs, exons with data frame operations in prepare-rpbp-genome

        This addresses Issue #33

    commit 311fce08c61085f808a8ecfb45b1c67c1bef6569
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Nov 13 19:52:18 2016 +0100

        FIX use logger in get-orf-peptide-matches

    commit fea8cac01ff7019d31d5b8649dbf713888385d51
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Nov 13 18:49:51 2016 +0100

        UPD print cmd for create-orf-profiles and create-base-genome-profile

    commit a7420e5f61394fb295388623b481a700eada197c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Nov 13 17:01:47 2016 +0100

        FIX renamed process-all-samples to run-all-rpbp-instances

    commit 65ef65bfd4c8b5ca0492636b39e460d2aa6719aa
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Nov 13 16:39:14 2016 +0100

        ADD scripts to extract, label ORFs without gffread

        This addresses Issue #18.

        This commit also includes several small fixes related to coordinating the
        filenames for using multimappers, as well as using the same reference files
        as ribo-te.

        Thus, it also addresses some small problems related to Issue #30.

        Conflicts:
        	rpbp/reference_preprocessing/prepare_genome.py
        	setup.py

    commit bf78a8b3a01be8b409d816249b165bd6626b096e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Nov 13 16:28:16 2016 +0100

        FIX "canonical" to "annotated" in create-orf-profiles

    commit 73bc029ec5f2feeb3d4d4778cedee0a7232e216f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Nov 10 16:30:54 2016 +0100

        FIX updated pipeline scripts to use new reference files

    commit ac5bae2204f2b93730ee04d47eb60a13b8faad21
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Nov 9 11:17:14 2016 +0100

        FIX metagene profiles explicitly use canonical ORFs only

    commit 174895ed5164e9e476c5873a803d8fc4d96785ef
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Nov 8 21:36:14 2016 +0100

        FIX incorrect is_unique flag in create-base-genome-profile

    commit a3905788d36de3e3d1ff0adb57f3ab74659bb2e1
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Nov 7 13:16:46 2016 +0100

        FIX added missing is_unique flag for finding periodic lengths and offsets

    commit 7c67025c285f885379b42e408b6a3e68380828dd
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Nov 7 09:54:44 2016 +0100

        FIX index star alignment file with multimappers

        This is necessaary in case multimappers are not removed; then the star
        alignment file is used downstream.

    commit 6cf7fde5731afbd8dc68aa541d26cbb9f9d67e47
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Nov 4 16:27:53 2016 +0100

        ADD option to keep multimapping riboseq reads

        This addresses Issue #30

    commit 1d556237b8b758451adf3ccc66bf7c5a0176f5e4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Nov 2 19:41:38 2016 +0100

        FIX logging statement in select-final-prediction-set

    commit c9d336da16661b0cb05e6d7ecd4d73061017189e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Nov 2 17:57:24 2016 +0100

        FIX using shell_utils in setup.py

    commit 25dcb366030fed683fc254de069ec9dacb0c0ccb
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Nov 2 17:53:38 2016 +0100

        FIX using shell_utils in prepare-genome

    commit dbf721f1b0b17bc0454400347616d50fef478697
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Nov 1 21:09:19 2016 +0100

        FIX added logging-utils to get-all-orf-peptide-matches

    commit 3fe98d920849ee68e4abe24fd75f8a151a192847
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Nov 1 19:34:06 2016 +0100

        FIX added logging_utils to get-orf-peptide-matches

    commit dcba047e422f29591bc6a652757af6bd060b1c3f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Nov 1 19:28:08 2016 +0100

        FIX peptide matches driver uses cell types and peptides specified in config

    commit 2f540496fc534cd0ddf10f330a3d5cb5063f41d5
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Nov 1 16:53:46 2016 +0100

        ADD script and notebook to visualize subcodon clusters

    commit 1c4ba2373757a6815c60af6e2dc9a077b9d20170
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Oct 31 21:17:35 2016 +0100

        FIX added top k% option for clustering subcodons

    commit 4773e4c4d3426e683eed1e2cc261354883f0b9de
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Oct 31 19:39:49 2016 +0100

        FIX changed subcodon clustering to pickle model

    commit 4fa1b4d8d7044a6668fe63e8fb597c880f3969bd
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Oct 31 17:23:58 2016 +0100

        FIX missing imports from cluster-subcodon-counts

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    Merge: d7375ed 8f47fc6
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Oct 31 15:58:56 2016 +0100

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit d7375ed9e0a11b720c641430acfff4002e1423d7
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Oct 31 15:58:31 2016 +0100

        ADD script to cluster and visualize subcodon counts

    commit 8f47fc68e2ca7f304527ac2cba528227f4e637d6
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Oct 12 11:38:24 2016 +0200

        FIX updated prediction reports to use shell_utils, etc.

    commit ba35bc2a0a5507c7846b6f7a2d3548f9492d687b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Oct 11 19:35:28 2016 +0200

        FIX updated scripts to delete intermediate files by default

    commit a75823d9906c639544196b78b1a46ae46a38e729
    Merge: e603fcb 7d6346e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Oct 4 19:47:39 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit e603fcb796a16a1ebd707966d638ffc16da3297d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Oct 4 19:47:29 2016 +0200

        Added slurm options for predictions report

    commit 7d6346e1991278f287389a23cfff0edb6161b6c2
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Sep 29 19:40:30 2016 +0200

        Added script to find differential micropeptides and related annotations

    commit 88e8549bdabf2e14f4ccdb706197fadabd7a0cc6
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:14:08 2016 +0200

        Fixed missing imports in preprocessing report

    commit 4b710318502b9722f3f8ab05976b1788f12a3c8e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:10:14 2016 +0200

        Added slurm options to preprocessing report

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    Merge: edad42e 473786a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:08:13 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit edad42e13364ce0dc791f2649cb844aa47fbf17b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:08:08 2016 +0200

        Updated read counting script to use logging_utils

    commit 4d1be9730ee05ac42b2741852dc986c50962cba0
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:07:21 2016 +0200

        Updated preprocessing report to use logging_utils

    commit 4adf88418a96a3858e9edf7309932f71b93e1202
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:04:18 2016 +0200

        Commented out call to extract-bed-sequences in prepare-genome.

        This call creates the transcripts fasta file, so the script does not run
        gffread. Once the new orf extraction process is finished, the call to gffread
        will be removed and this can be uncommented.

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:01:40 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 07002b2fafc437d38654814b435e8bfa9dac6693
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Sep 20 14:01:31 2016 +0200

        Added option to override the note for preprocessing report

    commit 948cb6a87026cfabf74fadf98d5a84ad8fadc1b3
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Sep 12 16:02:56 2016 +0200

        Added default number of yticks for visualizing read filtering counts

    commit 8ef286a08f76233cfc3fd588bfef325082840788
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    Date:   Fri Sep 9 17:31:56 2016 +0200

        Pulled minor release changes back in from master.

        Squashed commit of the following:

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            Update to setup

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                Added imports

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                Updated documentation

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                Minor update to notebook

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                Added --run-replicates option to run all samples and merge replicates

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                Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

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                Added analysis script to pull information about transcripts with ORFs from mygene

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                Updated preprocessing scripts to use new filenames

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            Author: Brandon Malone <bmmalone@gmail.com>
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                Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

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            Author: Brandon Malone <bmmalone@gmail.com>
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                Added option for including rp-chi in predictions report

            commit b2efe00abe40056502dd0d8ff722be6c4e919eb8
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                Fixed file checker for main profile script

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                Removed file checker for create-base-genome-profile.

                This is necessary because of the way "do-not-call" is handled for this type
                of external call. Also, create-base-genome-profile checks all of its files,
                so it should be unnecessary anyway.

            commit f20e745102cf5b32d35f02833ed29a7ca44b9885
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Aug 23 20:12:29 2016 +0200

                Added analysis script to remove peptide multimappers

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Aug 23 16:32:21 2016 +0200

                Update after merge

            commit 8db393c430b3af5d272d835ca80c081ab9c0b760
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Aug 23 16:31:10 2016 +0200

                Removed transcriptome alignment creation from base profile creation

            commit 6c6970ffafd42c74495a8f26ede418cf0e4f47f0
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 22:42:44 2016 +0200

                Fixed typo in system call

            commit 4abf3386e685583173561c3ff1c108d96ecc0b09
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 22:27:01 2016 +0200

                Changed metagene profile to use transcript bed12 file

            commit 33573124232b7672e57f02b2c03cb5b128a14604
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 22:25:58 2016 +0200

                Added call to create transcript bed12 file

            commit d8b3981d448d745547e8ee47607e7a581b2f794f
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 22:15:47 2016 +0200

                Removed metagene profile scripts (they are now in riboseq-utils)

            commit f87eaad38038aaac3543809869077f0626519fd6
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 21:59:36 2016 +0200

                Added file_checkers for most calls

            commit a7fc9c89a9b91111861d88ba3877592344ffb07a
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 21:39:11 2016 +0200

                Moved remove-multimapping-reads program to misc.bio_programs

            commit 7310a8aed10000c09c14c996ac59e50c0b83f1cf
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 21:08:14 2016 +0200

                Update

            commit 5dacb8b796dabc458010750a099542e3504d4da3
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 22 15:09:31 2016 +0200

                Removed bedtools as required programs

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            Date:   Mon Aug 22 15:08:56 2016 +0200

                Added file checkers to verify integrity of output files

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Aug 18 16:26:45 2016 +0200

                Updated BLAS installation instructions

            commit a291e935ea0b8abc002d2d30f3bb45ae8815c907
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Aug 16 14:14:40 2016 +0200

                Updated setup script to better handle existing imports

            commit bffd81f344a57477cdd10c092cd60bbf5d8af8c3
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Aug 15 16:21:50 2016 +0200

                Updated protein sequence data structure to match change in bio_utils

            commit cf680754d259a5ec9de0478889293ab188500a8f
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Aug 14 20:02:01 2016 +0200

                Fixed gffread import path to bio_utils

            commit 3d5eed507af0f9e2527b3e10ea43e76821afc943
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Aug 14 15:23:24 2016 +0200

                Changed logging completely to logging_utils

            commit ddaa70f17ebbdfec88345d5bb5f34947cf2de328
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Aug 14 14:25:16 2016 +0200

                Updated all scripts to use loggers

            commit d4b3800a29c8984518b83760bcf38efd0ed2cb4d
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Aug 14 13:48:31 2016 +0200

                Added command line options to control merging of predicted ORFs

            commit 041d272c27ca834777d8cc8bb18cd22a7bb59a02
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            Date:   Fri Aug 5 12:58:29 2016 +0200

                Updated ORF filtering to not combine out-of-frame reads for checking

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Wed Aug 3 18:06:22 2016 +0200

                Changed argument name from procs to cpus to be consistent with the rest of the package

            commit 874e407aff8270d939e1ece069b4e42ed53f9410
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Aug 2 21:01:08 2016 +0200

                Fixed output matrix dimension size

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Aug 2 12:05:43 2016 +0200

                Updated Mackowiak permutation test to use bed_utils from misc

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                Removed tmp from call to extract-orf-profiles

            commit 1e1ba6f041704adc017d5340b71285600ae3d462
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                Switched gffread header parsing to misc.gffread_utils function

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 31 18:31:04 2016 +0200

                Resolved import, etc., conflicts from merge

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 31 18:26:00 2016 +0200

                Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

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            Date:   Sun Jul 31 18:09:37 2016 +0200

                Fixed conflicts from merging branch

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 31 17:59:43 2016 +0200

                Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

            commit 5094314ec128950bf3ff66916eb895f3625cd0f9
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            Date:   Sat Jul 30 00:49:58 2016 +0200

                Fixed typo is viz script

            commit c13eea8c1ea614fb15b53ae31400c3f9f1417529
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 29 12:30:55 2016 +0200

                Updated notebook

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            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Jul 26 19:25:32 2016 +0200

                Fixed imports for permutation test temp files

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            Date:   Tue Jul 26 18:51:03 2016 +0200

                Added option to specify tmp directory for the permutation tests

            commit b588e2bd79494347f8af174264cfb2be96365c8b
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            Date:   Tue Jul 26 16:48:24 2016 +0200

                Added script to perform permutation test for determining significance of overlap with Mackowiak ORFs

            commit 081816a61c5cdedbafc0d5a48f2808ee6181591d
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 25 15:45:13 2016 +0200

                This commit adds scripts for matching the ORFs used in rpbp with QTI-seq peaks (from Gao et al.) and conserved small ORFs (from Mackowiak et al.).

            commit 53a96023ad9bfaef5ef0055bc3bc22a7ef9cbdcf
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            Date:   Thu Jul 14 14:22:39 2016 +0200

                Moved translational efficiency model to ribo-te project

            commit bee204b8838d385d590571146e07af71c063acf8
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jul 14 14:15:10 2016 +0200

                This merge replaces the parallel computing in estimate-bayes-factors with a shared memory approach.

                It addresses GitHub Issue #25.

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                    Added memory checking to estimate-orf-bayes-factors

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                This commit integrates smoothing into the Bayes factor estimation script.

                It addresses all of GitHub Issue #15 except the prediction report scripts. Those additions can be handled in a new branch later.

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                    Updated preprocessing report to use correct profiles files

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                    Updated pipeline scripts to properly handle smoothing as a part of BF estimation

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                    Added smoothing as a step of estimating Bayes factors

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                Updated setup to use ribo_filenames to find base models path

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                Updated installation instructions in README

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                This merge adds installation with pip (including --user).

                This addresses GitHub Issue #4.

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                    Started ignoring bak files

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                    Updated documentation to reflect new installation process

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                    Updated pipeline scripts to use default_models base

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                    Updated setup to correctly work with pip install

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                    Added external files to MANIFEST

                commit c73ccae7c5096c6ad420f03407e0f8542d087dfc
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                    Updated setup to use binary installs if possible

                commit d8b29bc713e9181635a136780d8656d44abcfe3c
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                    Updated setup to handle "internal" packages

            commit 766dacd7df58ffc343395d300128b9343c3b7bf2
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                Replaced fastqc for counting reads and alignments with misc.bio functions.

                Also cleaned up the preprocessing report to avoid wasted pages.

                This addresses GitHub Issue #16.

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            Date:   Fri Jul 8 19:15:18 2016 +0200

                This merge adds ORF type filtering to the predictions and the predictions report.

                It also cleans up the prediction report to avoid wasted space and latex compilation errors.

                This addresses GitHub Issue #19.

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                    Added filtered ORF type pie charts to predictions report (and cleaned up a few things in pipeline script)

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                Updated create-base-genome-profile script to use star_index.

                This was missing when GitHub Issue #8 was closed.

            commit bcde58dc5473a20208fe0628e08b65f7961b8523
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            Date:   Thu Jul 7 17:37:18 2016 +0200

                Fixed call in create-orf-profiles which resulted in the tmp directory 'None'.

                This also includes a fix for filenames in error messages in create-base-genome-profile.

                The addresses GitHub Issue #7.

            commit df2077b920dc654bf52687b8a349731755d512ea
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jul 7 15:33:25 2016 +0200

                Final commit to fix off-by-one error.

                This has now been tested on a wide array of datasets, and it appears to be stable.

                This completes GitHub Issue #5.

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                Updated rpkm-bf scatter plot to avoid missing files due to --merge-replicates

            commit 7fb19670b4dedf52f6beb87a8fc1539e4cc56fbb
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Wed Jul 6 14:03:11 2016 +0200

                This commit updates the behavior of STAR index creation to allow easier index reuse.

                It addresses GitHub Issue #8.

                Squashed commit of the following:

                commit 462b82959917571e7c89fe00fb1c3cc3b13ffae9
                Author: Brandon Malone <bmmalone@gmail.com>
                Date:   Wed Jul 6 14:01:53 2016 +0200

                    Updated documentation to reflect new behavior of STAR index creation

                commit e71a73ec9a0c3b5171ab61e61ef3dcc93b7141e6
                Author: Brandon Malone <bmmalone@gmail.com>
                Date:   Wed Jul 6 13:30:57 2016 +0200

                    Added check for star_index in all related scripts

                commit 1036f9b963e0a6005ab0e0ee540a8df14ded1092
                Author: Brandon Malone <bmmalone@gmail.com>
                Date:   Wed Jul 6 11:47:13 2016 +0200

                    Updated prepare-genome to use star_index, and to not use the gtf file as sjdb

            commit 3027e9684058481b77629105071de66fd0802e22
            Merge: e751cba f3831d5
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Jul 5 15:39:26 2016 +0200

                This merge includes the remaining pieces of the predictions report.

                It completes GitHub Issue #14.

                Merge branch 'create-predictions-report' into dev

                Conflicts:
                	rpbp/analysis/rpbp_predictions/visualize_orf_type_metagene_profiles.py

            commit f3831d5a02e8702028710dc82a5376a936eafbe4
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Jul 5 15:32:16 2016 +0200

                Added the RPKM-BF plots to the prediction report.

                This completes GitHub Issue #14.

            commit e751cbaefef7012c821c3aed0199cc5bce6ad499
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Jul 5 14:51:54 2016 +0200

                Added --merge-replicates behavior to the usage-instructions.

                This completes redmine Feature #100.

            commit 400ef8455149d052d304f398b2aa14caa3bf1431
            Merge: 5f5f0d4 dd26901
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Jul 5 14:42:21 2016 +0200

                This commit merges documentation updates for running the pipeline with --merge-replicates. It also includes several updates to the predictions report.

                This is a single commit due to poor branch management.

                Merge branch 'create-predictions-report' into dev

                Conflicts:
                	rpbp/analysis/rpbp_predictions/create_predictions_report.py

            commit dd26901ad57174e43331dff4f8de46fdbb824752
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Tue Jul 5 14:38:49 2016 +0200

                Updated description for running the example

            commit 894cd8926d9369397e14208ed535c362ca0718a9
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 19:28:34 2016 +0200

                Added script to create BF-RPKM scatter plots

            commit deeedc7c08241e949d3c2c2bd571417fd5de41b2
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 19:26:46 2016 +0200

                Fixed bug where chisq metagene profiles used smooth profiles

            commit 4f94a949c1429b4504fa7b8e94a9eb60bbfb77e6
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 19:26:10 2016 +0200

                Added bf-rpkm script to setup

            commit 06316755ca36b88e392157983ee7bf9aeb76bfec
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 19:17:25 2016 +0200

                Updated counting to use pysam rather than fastqc for counting read lengths

            commit 5f5f0d40f4e4accb34b0552a3ec4dc2b8db0fe8e
            Merge: 3f0ca21 a2f3c9a
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 14:35:30 2016 +0200

                Fixed merge conflict, which handles when some ORF profiles were not created

            commit a2f3c9a1b81d55389e41ca8857ed4e3611fedac1
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 14:31:01 2016 +0200

                Fixed data type bug in filtering ORF profiles

            commit 3f0ca21469cdbabc8675b889b26cbe5a933b8e91
            Merge: a87abba 730bcdf
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 14:28:28 2016 +0200

                Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

            commit a87abbabb6d16e48f983e1262ece54a3eaaf2255
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Mon Jul 4 00:22:43 2016 +0200

                Added metagene periodicity plots to preprocessing report.

                This addresses GitHub Issue #6

                Squashed commit of the following:

                commit 2fbaaf44d82fa55e0523bd8e34a6c7d2b978c249
                Author: Brandon Malone <bmmalone@gmail.com>
                Date:   Sun Jul 3 22:03:35 2016 +0200

                    Added ORF type periodicity to preprocessing report

                commit 730bcdf48b1ca2e2bb1c726ff2e3ff41d3d68422
                Author: Brandon Malone <bmmalone@gmail.com>
                Date:   Sun Jul 3 21:10:43 2016 +0200

                    Added filter to quickly find ORFs which meet minimum profile sum criterion

                commit 4392329abfde3218b1e1a5a0a6c60d7a26af2926
                Author: Brandon Malone <bmmalone@gmail.com>
                Date:   Sun Jul 3 18:34:45 2016 +0200

                    Updated ORF type metagene profiles to limit the required number of profiles

                commit dcc09da8571faa342fb2829d3d1b463400c7d46a
                Author: Brandon Malone <bmmalone@gmail.com>
                Date:   Sun Jul 3 17:50:50 2016 +0200

                    Fixed indexing error causing latex compilation error

            commit 2fbaaf44d82fa55e0523bd8e34a6c7d2b978c249
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 3 22:03:35 2016 +0200

                Added ORF type periodicity to preprocessing report

            commit 730bcdf48b1ca2e2bb1c726ff2e3ff41d3d68422
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 3 21:10:43 2016 +0200

                Added filter to quickly find ORFs which meet minimum profile sum criterion

            commit 4392329abfde3218b1e1a5a0a6c60d7a26af2926
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 3 18:34:45 2016 +0200

                Updated ORF type metagene profiles to limit the required number of profiles

            commit dcc09da8571faa342fb2829d3d1b463400c7d46a
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 3 17:50:50 2016 +0200

                Fixed indexing error causing latex compilation error

            commit 35fc0dcbe317af09d264a887353773f1e4e2bfc2
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 3 17:40:43 2016 +0200

                Fixed indexing error causing latex compilation error

            commit 85aa2d495bde4d13f45c74300947c3da290ea2d0
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 3 17:34:03 2016 +0200

                Added vim swp files to ignore list

            commit 0e25fbe4f19303ef3f660138ecbdd61e9843584d
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sun Jul 3 13:48:56 2016 +0200

                Added strands to ORF type pie chart.

                This addresses GitHub Issue #12.

            commit 6c41c624053e073a843348b5fc9d1e2b3951a2c4
            Merge: adb2cac a701616
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sat Jul 2 15:27:45 2016 +0200

                Merge branch 'create-predictions-report' into dev

            commit a7016161508076c0685a1aa6b8c7193eccb7dcbe
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sat Jul 2 15:27:00 2016 +0200

                Updated report to use agg backend for mpl

            commit adb2cac2a9ec812418598472955783d7352b7cb0
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Sat Jul 2 12:25:21 2016 +0200

                Updated merge-orfs to write gzipped mtx files

            commit 21ef26ae3f102c54808f156679aed2320beaa830
            Merge: 3cdc3c7 bd5acff
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 18:48:19 2016 +0200

                Merge branch 'rpchi-unsmoothed' into dev

                This merge completes Issue #3.

            commit bd5acff151f9ac494a1a4f5e5c820d223ab58399
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 18:47:53 2016 +0200

                Updated documents to explain that rpchi does not use smoothing

            commit 896726e28696417c9d7ff07d13352829e418b313
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 18:35:24 2016 +0200

                Updated predictions report to use unsmoothed profiles for rp-chi

            commit 2729ed5a4f4ad8932174e03171dc47722dca846c
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 18:33:46 2016 +0200

                Fixed error message when no ORFs of a given type are present

            commit 3cdc3c70ac417c6b1fa2da77444c9bf504379550
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 16:19:13 2016 +0200

                Updated the rp-chi predictions to use the unsmoothed profiles.

                This addresses the implementation work for GitHub Issue #3.

            commit 4b939bb2af03b8d513469a57bd4f2bac9fce166b
            Merge: 85364bd 3780c77
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 15:16:34 2016 +0200

                Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

            commit 3780c773109305aa9c7e24c9e3a8df1bb09eeb2c
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 15:00:36 2016 +0200

                The ORF profiles are gzipped before being written to disk.

                This addresses Redmine Feature #112.

            commit 85364bd0e6b8f7c458fea2d930e50fae0839a23f
            Merge: 8246756 38da983
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 14:14:09 2016 +0200

                Merge branch 'hotfix-reverse-strand-off-by-one' into dev

                This hotfix addresses github issue #5

            commit 38da98399498cd21b600f820e18c3dabe2f95889
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 14:13:10 2016 +0200

                Added patch to fix off-by-one error.

                It is unclear how stable this is, though, so metagene profiles by type diagnostics need to be used in the future to ensure we do not continue to see strand-specific biases.

            commit 8246756932043593167f6def151fc671c5ab6c7c
            Merge: d4ea23f a232b2b
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 14:06:35 2016 +0200

                These merges partially address the predictions report, Redmine Feature #121

                Merge branch 'create-predictions-report' into dev

            commit a232b2bb5db6fff9a018333e3e0cf6632c9a1d14
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 14:05:05 2016 +0200

                Added strand-specific metagene profiles

            commit c1d32e680a9ddc7bd1d46f9d73d6aeccec518a70
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Fri Jul 1 10:14:49 2016 +0200

                Added paths to metagene profile notebook

            commit 6a21f44bceb9e1843587b24e5784d1d1cc94631f
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jun 30 18:34:20 2016 +0200

                Shifted all negative strand P-sites forward (i.e., back, in relation to the ORFs) by one

            commit e016ac7663606b3bbed538cb9bc670b98e314073
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jun 30 18:28:04 2016 +0200

                Updated metagene profile notebook with an example checking strands

            commit 71e28ef5671fd979a95a402123f2f85c7807b25e
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jun 30 16:24:41 2016 +0200

                Added script to create ORF predictions analysis figures

            commit 4c23bba5fb6e77149249bb94abef3d98a663ca78
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jun 30 16:24:13 2016 +0200

                Added counts to orf type metagene profiles

            commit 60da14f65a6159cce854d5232c5eae1c910b6002
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jun 30 14:33:09 2016 +0200

                Added grouping option to length distribution script

            commit e5ebc82534353295fade941f3359869f80e37a1f
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Thu Jun 30 13:38:29 2016 +0200

                Added predictions report script to setup

            commit cf6d172e4842d51f5ce793e51383c992deaebffc
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Wed Jun 29 19:49:31 2016 +0200

                Added scripts to visualize orf types and lengths

            commit b1775aa69586c5fa6aca94e3ab61525effc380e8
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Wed Jun 29 16:02:13 2016 +0200

                Added orf type visualization script to setup

            commit 76d12e2c1fb2ca393e91ddc5c27da70ad372c599
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Wed Jun 29 16:01:04 2016 +0200

                Added script for orf type metagene profiles

            commit 13bc0e95362d70ba4552dbd2893a64fceeed5486
            Author: Brandon Malone <bmmalone@gmail.com>
            Date:   Wed Jun 29 16:00:41 2016 +0200

                Added notebook for orf type metagene profiles

    commit 55b512b85ccef3093ed640d6215ff38303be05e4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Sep 5 18:06:01 2016 +0200

        Added imports

    commit 64b957d76d987160746d762e4efaa323cba8f561
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Sep 4 13:43:34 2016 +0200

        Updated documentation

    commit 693581489f7f17e328bb71814dd8e9af53d7179c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Sep 4 13:05:59 2016 +0200

        Minor update to notebook

    commit 452bc0a4aa6872e5a5481f9c974c801266830ccd
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Sep 4 13:04:53 2016 +0200

        Added --run-replicates option to run all samples and merge replicates

    commit 4134142229e33314226690e1791cd9e5bccb3b7b
    Merge: b9abc18 889ced5
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Sep 2 19:28:34 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit b9abc1815808a57153dc34edab1e3ac3298033d2
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Sep 2 19:28:27 2016 +0200

        Added analysis script to pull information about transcripts with ORFs from mygene

    commit 889ced50e8014ae71e7f8c21e3d9ccb82df10787
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 25 15:49:29 2016 +0200

        Updated preprocessing scripts to use new filenames

    commit 347833fdf3f024cd54c590987a7b96ceb59770f0
    Merge: 195c54a b2efe00
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 25 11:01:19 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 195c54a40908ef94bb4b5f5a93f1af0b04bc1a02
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 25 11:00:33 2016 +0200

        Added option for including rp-chi in predictions report

    commit b2efe00abe40056502dd0d8ff722be6c4e919eb8
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Aug 24 11:49:16 2016 +0200

        Fixed file checker for main profile script

    commit 103efe2abe5e0cfc4a9faa4bdd2bcc95bf059d9f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Aug 24 10:43:31 2016 +0200

        Removed file checker for create-base-genome-profile.

        This is necessary because of the way "do-not-call" is handled for this type
        of external call. Also, create-base-genome-profile checks all of its files,
        so it should be unnecessary anyway.

    commit f20e745102cf5b32d35f02833ed29a7ca44b9885
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 23 20:12:29 2016 +0200

        Added analysis script to remove peptide multimappers

    commit 197c2b185506c8106feaca1b6590043c06c2fffe
    Merge: 8db393c 6c6970f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 23 16:32:21 2016 +0200

        Update after merge

    commit 8db393c430b3af5d272d835ca80c081ab9c0b760
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 23 16:31:10 2016 +0200

        Removed transcriptome alignment creation from base profile creation

    commit 6c6970ffafd42c74495a8f26ede418cf0e4f47f0
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:42:44 2016 +0200

        Fixed typo in system call

    commit 4abf3386e685583173561c3ff1c108d96ecc0b09
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:27:01 2016 +0200

        Changed metagene profile to use transcript bed12 file

    commit 33573124232b7672e57f02b2c03cb5b128a14604
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:25:58 2016 +0200

        Added call to create transcript bed12 file

    commit d8b3981d448d745547e8ee47607e7a581b2f794f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:15:47 2016 +0200

        Removed metagene profile scripts (they are now in riboseq-utils)

    commit f87eaad38038aaac3543809869077f0626519fd6
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 21:59:36 2016 +0200

        Added file_checkers for most calls

    commit a7fc9c89a9b91111861d88ba3877592344ffb07a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 21:39:11 2016 +0200

        Moved remove-multimapping-reads program to misc.bio_programs

    commit 7310a8aed10000c09c14c996ac59e50c0b83f1cf
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 21:08:14 2016 +0200

        Update

    commit 5dacb8b796dabc458010750a099542e3504d4da3
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 15:09:31 2016 +0200

        Removed bedtools as required programs

    commit 64de186bed7864a7ce0a82b29fe7bef62658c0e7
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 15:08:56 2016 +0200

        Added file checkers to verify integrity of output files

    commit 3f72de72bf7e29af9fa2da1b16d72fe59cb2980f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 18 16:26:45 2016 +0200

        Updated BLAS installation instructions

    commit a291e935ea0b8abc002d2d30f3bb45ae8815c907
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 16 14:14:40 2016 +0200

        Updated setup script to better handle existing imports

    commit bffd81f344a57477cdd10c092cd60bbf5d8af8c3
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 15 16:21:50 2016 +0200

        Updated protein sequence data structure to match change in bio_utils

    commit cf680754d259a5ec9de0478889293ab188500a8f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 20:02:01 2016 +0200

        Fixed gffread import path to bio_utils

    commit 3d5eed507af0f9e2527b3e10ea43e76821afc943
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 15:23:24 2016 +0200

        Changed logging completely to logging_utils

    commit ddaa70f17ebbdfec88345d5bb5f34947cf2de328
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 14:25:16 2016 +0200

        Updated all scripts to use loggers

    commit d4b3800a29c8984518b83760bcf38efd0ed2cb4d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 13:48:31 2016 +0200

        Added command line options to control merging of predicted ORFs

    commit 041d272c27ca834777d8cc8bb18cd22a7bb59a02
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Aug 5 12:58:29 2016 +0200

        Updated ORF filtering to not combine out-of-frame reads for checking

    commit a2289b07b5d58b6ba47188f7a68b66ed2506a2f4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Aug 3 18:06:22 2016 +0200

        Changed argument name from procs to cpus to be consistent with the rest of the package

    commit 874e407aff8270d939e1ece069b4e42ed53f9410
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 2 21:01:08 2016 +0200

        Fixed output matrix dimension size

    commit 8568523dac481a2a75d1a1f6fe51d6ed13d20b9d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 2 12:05:43 2016 +0200

        Updated Mackowiak permutation test to use bed_utils from misc

    commit 4417cbe940347825a05c5ff600f02a9d4077b0c4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 1 00:28:07 2016 +0200

        Removed tmp from call to extract-orf-profiles

    commit 1e1ba6f041704adc017d5340b71285600ae3d462
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 19:25:36 2016 +0200

        Switched gffread header parsing to misc.gffread_utils function

    commit cbf6af6354975b4a4c83f1f00395b19fccc4d2ad
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 18:31:04 2016 +0200

        Resolved import, etc., conflicts from merge

    commit 5a50529ab137cbe7420415f6c65caadf98b07b82
    Merge: 5094314 5ec1eca
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 18:26:00 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 5ec1eca3a121757974a2302295bd441643a76072
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 18:09:37 2016 +0200

        Fixed conflicts from merging branch

    commit 5e211142ebc41ec860b8c5eb5581938b90ec447d
    Merge: c13eea8 84c5198
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 17:59:43 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 5094314ec128950bf3ff66916eb895f3625cd0f9
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Jul 30 00:49:58 2016 +0200

        Fixed typo is viz script

    commit c13eea8c1ea614fb15b53ae31400c3f9f1417529
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 29 12:30:55 2016 +0200

        Updated notebook

    commit 84c5198a2eee6abf988c71f4e93b3a8c78f737dc
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 26 19:25:32 2016 +0200

        Fixed imports for permutation test temp files

    commit bd7a3fa6235ceda6d47fdea3e98f579c38a25974
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 26 18:51:03 2016 +0200

        Added option to specify tmp directory for the permutation tests

    commit b588e2bd79494347f8af174264cfb2be96365c8b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 26 16:48:24 2016 +0200

        Added script to perform permutation test for determining significance of overlap with Mackowiak ORFs

    commit 081816a61c5cdedbafc0d5a48f2808ee6181591d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 25 15:45:13 2016 +0200

        This commit adds scripts for matching the ORFs used in rpbp with QTI-seq peaks (from Gao et al.) and conserved small ORFs (from Mackowiak et al.).

    commit 53a96023ad9bfaef5ef0055bc3bc22a7ef9cbdcf
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        Moved translational efficiency model to ribo-te project

    commit bee204b8838d385d590571146e07af71c063acf8
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    Date:   Thu Jul 14 14:15:10 2016 +0200

        This merge replaces the parallel computing in estimate-bayes-factors with a shared memory approach.

        It addresses GitHub Issue #25.

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        This commit integrates smoothing into the Bayes factor estimation script.

        It addresses all of GitHub Issue #15 except the prediction report scripts. Those additions can be handled in a new branch later.

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        Updated installation instructions in README

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        This merge adds installation with pip (including --user).

        This addresses GitHub Issue #4.

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            Updated setup to use binary installs if possible

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        Also cleaned up the preprocessing report to avoid wasted pages.

        This addresses GitHub Issue #16.

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        This merge adds ORF type filtering to the predictions and the predictions report.

        It also cleans up the prediction report to avoid wasted space and latex compilation errors.

        This addresses GitHub Issue #19.

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        This was missing when GitHub Issue #8 was closed.

    commit bcde58dc5473a20208fe0628e08b65f7961b8523
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        Fixed call in create-orf-profiles which resulted in the tmp directory 'None'.

        This also includes a fix for filenames in error messages in create-base-genome-profile.

        The addresses GitHub Issue #7.

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    Date:   Thu Jul 7 15:33:25 2016 +0200

        Final commit to fix off-by-one error.

        This has now been tested on a wide array of datasets, and it appears to be stable.

        This completes GitHub Issue #5.

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        This commit updates the behavior of STAR index creation to allow easier index reuse.

        It addresses GitHub Issue #8.

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            Updated prepare-genome to use star_index, and to not use the gtf file as sjdb

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    Author: Brandon Malone <bmmalone@gmail.com>
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        This merge includes the remaining pieces of the predictions report.

        It completes GitHub Issue #14.

        Merge branch 'create-predictions-report' into dev

        Conflicts:
        	rpbp/analysis/rpbp_predictions/visualize_orf_type_metagene_profiles.py

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    Date:   Tue Jul 5 15:32:16 2016 +0200

        Added the RPKM-BF plots to the prediction report.

        This completes GitHub Issue #14.

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        Added --merge-replicates behavior to the usage-instructions.

        This completes redmine Feature #100.

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 5 14:42:21 2016 +0200

        This commit merges documentation updates for running the pipeline with --merge-replicates. It also includes several updates to the predictions report.

        This is a single commit due to poor branch management.

        Merge branch 'create-predictions-report' into dev

        Conflicts:
        	rpbp/analysis/rpbp_predictions/create_predictions_report.py

    commit dd26901ad57174e43331dff4f8de46fdbb824752
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 5 14:38:49 2016 +0200

        Updated description for running the example

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    Date:   Mon Jul 4 19:28:34 2016 +0200

        Added script to create BF-RPKM scatter plots

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    Date:   Mon Jul 4 19:26:46 2016 +0200

        Fixed bug where chisq metagene profiles used smooth profiles

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    Date:   Mon Jul 4 19:26:10 2016 +0200

        Added bf-rpkm script to setup

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    Date:   Mon Jul 4 19:17:25 2016 +0200

        Updated counting to use pysam rather than fastqc for counting read lengths

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    Date:   Mon Jul 4 14:35:30 2016 +0200

        Fixed merge conflict, which handles when some ORF profiles were not created

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 14:31:01 2016 +0200

        Fixed data type bug in filtering ORF profiles

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 14:28:28 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

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    Date:   Mon Jul 4 00:22:43 2016 +0200

        Added metagene periodicity plots to preprocessing report.

        This addresses GitHub Issue #6

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            Updated ORF type metagene profiles to limit the required number of profiles

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        Added ORF type periodicity to preprocessing report

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        Added filter to quickly find ORFs which meet minimum profile sum criterion

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        Updated ORF type metagene profiles to limit the required number of profiles

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        Fixed indexing error causing latex compilation error

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        Fixed indexing error causing latex compilation error

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        Added vim swp files to ignore list

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        Added strands to ORF type pie chart.

        This addresses GitHub Issue #12.

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        Merge branch 'create-predictions-report' into dev

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        Updated report to use agg backend for mpl

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        Updated merge-orfs to write gzipped mtx files

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    Merge: 3cdc3c7 bd5acff
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 18:48:19 2016 +0200

        Merge branch 'rpchi-unsmoothed' into dev

        This merge completes Issue #3.

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    Date:   Fri Jul 1 18:47:53 2016 +0200

        Updated documents to explain that rpchi does not use smoothing

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    Date:   Fri Jul 1 18:35:24 2016 +0200

        Updated predictions report to use unsmoothed profiles for rp-chi

    commit 2729ed5a4f4ad8932174e03171dc47722dca846c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 18:33:46 2016 +0200

        Fixed error message when no ORFs of a given type are present

    commit 3cdc3c70ac417c6b1fa2da77444c9bf504379550
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 16:19:13 2016 +0200

        Updated the rp-chi predictions to use the unsmoothed profiles.

        This addresses the implementation work for GitHub Issue #3.

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    Merge: 85364bd 3780c77
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 15:16:34 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 3780c773109305aa9c7e24c9e3a8df1bb09eeb2c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 15:00:36 2016 +0200

        The ORF profiles are gzipped before being written to disk.

        This addresses Redmine Feature #112.

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    Merge: 8246756 38da983
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:14:09 2016 +0200

        Merge branch 'hotfix-reverse-strand-off-by-one' into dev

        This hotfix addresses github issue #5

    commit 38da98399498cd21b600f820e18c3dabe2f95889
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:13:10 2016 +0200

        Added patch to fix off-by-one error.

        It is unclear how stable this is, though, so metagene profiles by type diagnostics need to be used in the future to ensure we do not continue to see strand-specific biases.

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:06:35 2016 +0200

        These merges partially address the predictions report, Redmine Feature #121

        Merge branch 'create-predictions-report' into dev

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:05:05 2016 +0200

        Added strand-specific metagene profiles

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 10:14:49 2016 +0200

        Added paths to metagene profile notebook

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 18:34:20 2016 +0200

        Shifted all negative strand P-sites forward (i.e., back, in relation to the ORFs) by one

    commit e016ac7663606b3bbed538cb9bc670b98e314073
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 18:28:04 2016 +0200

        Updated metagene profile notebook with an example checking strands

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    Date:   Thu Jun 30 16:24:41 2016 +0200

        Added script to create ORF predictions analysis figures

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    Date:   Thu Jun 30 16:24:13 2016 +0200

        Added counts to orf type metagene profiles

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    Date:   Thu Jun 30 14:33:09 2016 +0200

        Added grouping option to length distribution script

    commit e5ebc82534353295fade941f3359869f80e37a1f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 13:38:29 2016 +0200

        Added predictions report script to setup

    commit cf6d172e4842d51f5ce793e51383c992deaebffc
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jun 29 19:49:31 2016 +0200

        Added scripts to visualize orf types and lengths

    commit b1775aa69586c5fa6aca94e3ab61525effc380e8
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    Date:   Wed Jun 29 16:02:13 2016 +0200

        Added orf type visualization script to setup

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    Date:   Wed Jun 29 16:01:04 2016 +0200

        Added script for orf type metagene profiles

    commit 13bc0e95362d70ba4552dbd2893a64fceeed5486
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    Date:   Wed Jun 29 16:00:41 2016 +0200

        Added notebook for orf type metagene profiles

commit 8cb350891f5e72b20e53836796d6c3031acc7f3d
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Wed Mar 29 18:13:31 2017 +0200

    DEL old predictions report

commit 9b8082732479d985247af6540314f184d61a7b0b
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Wed Mar 29 18:11:57 2017 +0200

    MNT merge with dev for version 1.1.5

    Conflicts:
    	CHANGELOG.md
    	docs/custom-alignment-files.html
    	docs/installation.html
    	docs/running-example.html
    	docs/usage-instructions.html
    	docs/usage-instructions.md
    	notebooks/rpbp-predictions/create-orf-type-pie-chart.ipynb
    	rpbp/__init__.py
    	rpbp/analysis/profile_construction/create_preprocessing_report.py
    	rpbp/analysis/profile_construction/create_read_length_metagene_profile_plot.py
    	rpbp/analysis/profile_construction/get_all_read_filtering_counts.py
    	rpbp/reference_preprocessing/prepare_rpbp_genome.py
    	rpbp/run_all_rpbp_instances.py
    	rpbp/run_rpbp_pipeline.py
    	setup.py

commit 91181cb242c678d72dc03b1aa094ca06a6090aca
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Wed Feb 22 17:14:59 2017 +0100

    MNT Update to version 1.1.4

    Squashed commit of the following:

    commit af39a056e3ae70cd9a42db9b362eafa9887f800b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Feb 22 11:43:53 2017 +0100

        MNT removed [analysis] optional package

        This addresses issue #56 and includes a minor version bump

commit 64cc2f14b56bc3d7588e509c0a9b7bee8f6f77ba
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Tue Feb 21 22:27:36 2017 +0100

    FIX compiling Stan models with spaces in paths

    This is again related to Issue #36. The change log includes more details.

commit a74c76813d3f3ebbdd85df477d0e9be410d84647
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Thu Feb 16 09:58:12 2017 +0100

    MNT merged version 1.1.2 from dev

    This is mostly in response to Issue #51.

    Conflicts:
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    	docs/installation.md
    	rpbp/process_all_samples.py
    	rpbp/process_all_samples.py.bak
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commit 5f101be1bd52448e93c764a9cca77996580eaff1
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Wed Feb 15 00:11:36 2017 +0100

    UPD bump change log

commit 78783b01ef6eea58f90f64c960d29dba2011f4bd
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Tue Feb 14 23:09:52 2017 +0100

    UPD cleaning documentation

commit 30c297dec2032212a81622837e4e7a60413e984c
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Tue Feb 14 20:52:22 2017 +0100

    UPD resolve conflicts from dev for version 1.1

commit 538eedaec94b0aed7a4b60dfc85e113dd46b4979
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Wed Feb 1 20:51:02 2017 +0100

    UPD minor version bump

commit 235a1a1567c3870e9a1814b238b8c2d81d9f478f
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Wed Feb 1 20:49:30 2017 +0100

    FIX model compilation failed with spaces in path

    This addresses Issue #36.

commit 287bf022d0924e83a0ef5cf4a0570258de0f0c4e
Author: bmmalone <bmmalone@gmail.com>
Date:   Tue Sep 6 14:32:20 2016 +0200

    Update running-example.md

commit 645c3daa9f538e63ea69f5011e8f2c6ad1ef5b2f
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Mon Sep 5 18:08:37 2016 +0200

    Update to setup

commit 5ab78989334bb04bc28a27379c3de590534a09ea
Author: Brandon Malone <bmmalone@gmail.com>
Date:   Mon Sep 5 18:06:40 2016 +0200

    Squashed commit of the following:

    commit 55b512b85ccef3093ed640d6215ff38303be05e4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Sep 5 18:06:01 2016 +0200

        Added imports

    commit 64b957d76d987160746d762e4efaa323cba8f561
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Sep 4 13:43:34 2016 +0200

        Updated documentation

    commit 693581489f7f17e328bb71814dd8e9af53d7179c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Sep 4 13:05:59 2016 +0200

        Minor update to notebook

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Sep 4 13:04:53 2016 +0200

        Added --run-replicates option to run all samples and merge replicates

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    Merge: b9abc18 889ced5
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Sep 2 19:28:34 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit b9abc1815808a57153dc34edab1e3ac3298033d2
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Sep 2 19:28:27 2016 +0200

        Added analysis script to pull information about transcripts with ORFs from mygene

    commit 889ced50e8014ae71e7f8c21e3d9ccb82df10787
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 25 15:49:29 2016 +0200

        Updated preprocessing scripts to use new filenames

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    Merge: 195c54a b2efe00
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 25 11:01:19 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 195c54a40908ef94bb4b5f5a93f1af0b04bc1a02
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 25 11:00:33 2016 +0200

        Added option for including rp-chi in predictions report

    commit b2efe00abe40056502dd0d8ff722be6c4e919eb8
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Aug 24 11:49:16 2016 +0200

        Fixed file checker for main profile script

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Aug 24 10:43:31 2016 +0200

        Removed file checker for create-base-genome-profile.

        This is necessary because of the way "do-not-call" is handled for this type
        of external call. Also, create-base-genome-profile checks all of its files,
        so it should be unnecessary anyway.

    commit f20e745102cf5b32d35f02833ed29a7ca44b9885
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 23 20:12:29 2016 +0200

        Added analysis script to remove peptide multimappers

    commit 197c2b185506c8106feaca1b6590043c06c2fffe
    Merge: 8db393c 6c6970f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 23 16:32:21 2016 +0200

        Update after merge

    commit 8db393c430b3af5d272d835ca80c081ab9c0b760
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 23 16:31:10 2016 +0200

        Removed transcriptome alignment creation from base profile creation

    commit 6c6970ffafd42c74495a8f26ede418cf0e4f47f0
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:42:44 2016 +0200

        Fixed typo in system call

    commit 4abf3386e685583173561c3ff1c108d96ecc0b09
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:27:01 2016 +0200

        Changed metagene profile to use transcript bed12 file

    commit 33573124232b7672e57f02b2c03cb5b128a14604
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:25:58 2016 +0200

        Added call to create transcript bed12 file

    commit d8b3981d448d745547e8ee47607e7a581b2f794f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 22:15:47 2016 +0200

        Removed metagene profile scripts (they are now in riboseq-utils)

    commit f87eaad38038aaac3543809869077f0626519fd6
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 21:59:36 2016 +0200

        Added file_checkers for most calls

    commit a7fc9c89a9b91111861d88ba3877592344ffb07a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 21:39:11 2016 +0200

        Moved remove-multimapping-reads program to misc.bio_programs

    commit 7310a8aed10000c09c14c996ac59e50c0b83f1cf
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 21:08:14 2016 +0200

        Update

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 15:09:31 2016 +0200

        Removed bedtools as required programs

    commit 64de186bed7864a7ce0a82b29fe7bef62658c0e7
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 22 15:08:56 2016 +0200

        Added file checkers to verify integrity of output files

    commit 3f72de72bf7e29af9fa2da1b16d72fe59cb2980f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Aug 18 16:26:45 2016 +0200

        Updated BLAS installation instructions

    commit a291e935ea0b8abc002d2d30f3bb45ae8815c907
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 16 14:14:40 2016 +0200

        Updated setup script to better handle existing imports

    commit bffd81f344a57477cdd10c092cd60bbf5d8af8c3
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 15 16:21:50 2016 +0200

        Updated protein sequence data structure to match change in bio_utils

    commit cf680754d259a5ec9de0478889293ab188500a8f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 20:02:01 2016 +0200

        Fixed gffread import path to bio_utils

    commit 3d5eed507af0f9e2527b3e10ea43e76821afc943
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 15:23:24 2016 +0200

        Changed logging completely to logging_utils

    commit ddaa70f17ebbdfec88345d5bb5f34947cf2de328
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 14:25:16 2016 +0200

        Updated all scripts to use loggers

    commit d4b3800a29c8984518b83760bcf38efd0ed2cb4d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Aug 14 13:48:31 2016 +0200

        Added command line options to control merging of predicted ORFs

    commit 041d272c27ca834777d8cc8bb18cd22a7bb59a02
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Aug 5 12:58:29 2016 +0200

        Updated ORF filtering to not combine out-of-frame reads for checking

    commit a2289b07b5d58b6ba47188f7a68b66ed2506a2f4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Aug 3 18:06:22 2016 +0200

        Changed argument name from procs to cpus to be consistent with the rest of the package

    commit 874e407aff8270d939e1ece069b4e42ed53f9410
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 2 21:01:08 2016 +0200

        Fixed output matrix dimension size

    commit 8568523dac481a2a75d1a1f6fe51d6ed13d20b9d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Aug 2 12:05:43 2016 +0200

        Updated Mackowiak permutation test to use bed_utils from misc

    commit 4417cbe940347825a05c5ff600f02a9d4077b0c4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Aug 1 00:28:07 2016 +0200

        Removed tmp from call to extract-orf-profiles

    commit 1e1ba6f041704adc017d5340b71285600ae3d462
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 19:25:36 2016 +0200

        Switched gffread header parsing to misc.gffread_utils function

    commit cbf6af6354975b4a4c83f1f00395b19fccc4d2ad
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 18:31:04 2016 +0200

        Resolved import, etc., conflicts from merge

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    Merge: 5094314 5ec1eca
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 18:26:00 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 5ec1eca3a121757974a2302295bd441643a76072
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 18:09:37 2016 +0200

        Fixed conflicts from merging branch

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    Merge: c13eea8 84c5198
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 31 17:59:43 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 5094314ec128950bf3ff66916eb895f3625cd0f9
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Jul 30 00:49:58 2016 +0200

        Fixed typo is viz script

    commit c13eea8c1ea614fb15b53ae31400c3f9f1417529
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 29 12:30:55 2016 +0200

        Updated notebook

    commit 84c5198a2eee6abf988c71f4e93b3a8c78f737dc
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 26 19:25:32 2016 +0200

        Fixed imports for permutation test temp files

    commit bd7a3fa6235ceda6d47fdea3e98f579c38a25974
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 26 18:51:03 2016 +0200

        Added option to specify tmp directory for the permutation tests

    commit b588e2bd79494347f8af174264cfb2be96365c8b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 26 16:48:24 2016 +0200

        Added script to perform permutation test for determining significance of overlap with Mackowiak ORFs

    commit 081816a61c5cdedbafc0d5a48f2808ee6181591d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 25 15:45:13 2016 +0200

        This commit adds scripts for matching the ORFs used in rpbp with QTI-seq peaks (from Gao et al.) and conserved small ORFs (from Mackowiak et al.).

    commit 53a96023ad9bfaef5ef0055bc3bc22a7ef9cbdcf
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jul 14 14:22:39 2016 +0200

        Moved translational efficiency model to ribo-te project

    commit bee204b8838d385d590571146e07af71c063acf8
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jul 14 14:15:10 2016 +0200

        This merge replaces the parallel computing in estimate-bayes-factors with a shared memory approach.

        It addresses GitHub Issue #25.

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        Author: Brandon Malone <bmmalone@gmail.com>
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            Updated shared memory to use multiprocessing.RawValue and global variables (as suggested on StackOverflow)

        commit 3fab0f6b06b3f357ea4ff981fb62b61413da65ca
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        Author: Brandon Malone <bmmalone@gmail.com>
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            Added memory checking to estimate-orf-bayes-factors

    commit a9036e61ba8889ec9b139ee1969f18dfc18632b8
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jul 13 15:03:03 2016 +0200

        This commit integrates smoothing into the Bayes factor estimation script.

        It addresses all of GitHub Issue #15 except the prediction report scripts. Those additions can be handled in a new branch later.

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            Updated filtering to avoid unnecessary reallocations

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        Author: Brandon Malone <bmmalone@gmail.com>
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            Updated preprocessing report to use correct profiles files

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            Updated pipeline scripts to properly handle smoothing as a part of BF estimation

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            Removed smoothing from profile construction

        commit 984ddd4523a95b937aef2e880305748ddbb26f90
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        Date:   Tue Jul 12 16:40:36 2016 +0200

            Added smoothing as a step of estimating Bayes factors

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        Updated setup to use ribo_filenames to find base models path

    commit 1d58e425dfd1275946398a171c560cc2f9b62354
    Author: Brandon Malone <bmmalone@gmail.com>
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        Updated installation instructions in README

    commit 0a26d5fe3cd1f2ee13981b0f2618dbca01fc5587
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Jul 9 15:51:00 2016 +0200

        This merge adds installation with pip (including --user).

        This addresses GitHub Issue #4.

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            Started ignoring scratch notebooks

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            Started ignoring bak files

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        Author: Brandon Malone <bmmalone@gmail.com>
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            Updated documentation to reflect new installation process

        commit 4dc2b1a05914e87b50761a2509842e00085deaa8
        Author: Brandon Malone <bmmalone@gmail.com>
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            Updated pipeline scripts to use default_models base

        commit dcb8d3d9a520ef03d56a6cc13f2ae0ae55095e9c
        Author: Brandon Malone <bmmalone@gmail.com>
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            Updated setup to correctly work with pip install

        commit ca19b8f53901d99de93d42777be5e805e15c5781
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            Added external files to MANIFEST

        commit c73ccae7c5096c6ad420f03407e0f8542d087dfc
        Author: Brandon Malone <bmmalone@gmail.com>
        Date:   Fri Jul 8 13:30:09 2016 +0200

            Updated setup to use binary installs if possible

        commit d8b29bc713e9181635a136780d8656d44abcfe3c
        Author: Brandon Malone <bmmalone@gmail.com>
        Date:   Wed Jul 6 11:23:58 2016 +0200

            Updated setup to handle "internal" packages

    commit 766dacd7df58ffc343395d300128b9343c3b7bf2
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 8 21:17:11 2016 +0200

        Replaced fastqc for counting reads and alignments with misc.bio functions.

        Also cleaned up the preprocessing report to avoid wasted pages.

        This addresses GitHub Issue #16.

    commit b86c33d612a3655a6d86bc8b4c217682c1dfe7a9
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 8 19:15:18 2016 +0200

        This merge adds ORF type filtering to the predictions and the predictions report.

        It also cleans up the prediction report to avoid wasted space and latex compilation errors.

        This addresses GitHub Issue #19.

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            Updated predictions report to avoid excessive wasted pages

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            Added filtered ORF type pie charts to predictions report (and cleaned up a few things in pipeline script)

        commit 4914c5b18507b52b45ee46d1566da000dea9e936
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            Added ORF type filter for predictions to pipeline script

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            Added ORF type filtering to selecting the prediction set

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    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 8 14:48:46 2016 +0200

        Updated create-base-genome-profile script to use star_index.

        This was missing when GitHub Issue #8 was closed.

    commit bcde58dc5473a20208fe0628e08b65f7961b8523
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jul 7 17:37:18 2016 +0200

        Fixed call in create-orf-profiles which resulted in the tmp directory 'None'.

        This also includes a fix for filenames in error messages in create-base-genome-profile.

        The addresses GitHub Issue #7.

    commit df2077b920dc654bf52687b8a349731755d512ea
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jul 7 15:33:25 2016 +0200

        Final commit to fix off-by-one error.

        This has now been tested on a wide array of datasets, and it appears to be stable.

        This completes GitHub Issue #5.

    commit fa7d52a77af107fc0cfb5843fc42e1037c12d245
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jul 6 14:07:20 2016 +0200

        Updated rpkm-bf scatter plot to avoid missing files due to --merge-replicates

    commit 7fb19670b4dedf52f6beb87a8fc1539e4cc56fbb
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jul 6 14:03:11 2016 +0200

        This commit updates the behavior of STAR index creation to allow easier index reuse.

        It addresses GitHub Issue #8.

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        Author: Brandon Malone <bmmalone@gmail.com>
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            Updated documentation to reflect new behavior of STAR index creation

        commit e71a73ec9a0c3b5171ab61e61ef3dcc93b7141e6
        Author: Brandon Malone <bmmalone@gmail.com>
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            Added check for star_index in all related scripts

        commit 1036f9b963e0a6005ab0e0ee540a8df14ded1092
        Author: Brandon Malone <bmmalone@gmail.com>
        Date:   Wed Jul 6 11:47:13 2016 +0200

            Updated prepare-genome to use star_index, and to not use the gtf file as sjdb

    commit 3027e9684058481b77629105071de66fd0802e22
    Merge: e751cba f3831d5
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 5 15:39:26 2016 +0200

        This merge includes the remaining pieces of the predictions report.

        It completes GitHub Issue #14.

        Merge branch 'create-predictions-report' into dev

        Conflicts:
        	rpbp/analysis/rpbp_predictions/visualize_orf_type_metagene_profiles.py

    commit f3831d5a02e8702028710dc82a5376a936eafbe4
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 5 15:32:16 2016 +0200

        Added the RPKM-BF plots to the prediction report.

        This completes GitHub Issue #14.

    commit e751cbaefef7012c821c3aed0199cc5bce6ad499
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 5 14:51:54 2016 +0200

        Added --merge-replicates behavior to the usage-instructions.

        This completes redmine Feature #100.

    commit 400ef8455149d052d304f398b2aa14caa3bf1431
    Merge: 5f5f0d4 dd26901
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 5 14:42:21 2016 +0200

        This commit merges documentation updates for running the pipeline with --merge-replicates. It also includes several updates to the predictions report.

        This is a single commit due to poor branch management.

        Merge branch 'create-predictions-report' into dev

        Conflicts:
        	rpbp/analysis/rpbp_predictions/create_predictions_report.py

    commit dd26901ad57174e43331dff4f8de46fdbb824752
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Tue Jul 5 14:38:49 2016 +0200

        Updated description for running the example

    commit 894cd8926d9369397e14208ed535c362ca0718a9
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 19:28:34 2016 +0200

        Added script to create BF-RPKM scatter plots

    commit deeedc7c08241e949d3c2c2bd571417fd5de41b2
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 19:26:46 2016 +0200

        Fixed bug where chisq metagene profiles used smooth profiles

    commit 4f94a949c1429b4504fa7b8e94a9eb60bbfb77e6
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 19:26:10 2016 +0200

        Added bf-rpkm script to setup

    commit 06316755ca36b88e392157983ee7bf9aeb76bfec
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 19:17:25 2016 +0200

        Updated counting to use pysam rather than fastqc for counting read lengths

    commit 5f5f0d40f4e4accb34b0552a3ec4dc2b8db0fe8e
    Merge: 3f0ca21 a2f3c9a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 14:35:30 2016 +0200

        Fixed merge conflict, which handles when some ORF profiles were not created

    commit a2f3c9a1b81d55389e41ca8857ed4e3611fedac1
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 14:31:01 2016 +0200

        Fixed data type bug in filtering ORF profiles

    commit 3f0ca21469cdbabc8675b889b26cbe5a933b8e91
    Merge: a87abba 730bcdf
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 14:28:28 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit a87abbabb6d16e48f983e1262ece54a3eaaf2255
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Mon Jul 4 00:22:43 2016 +0200

        Added metagene periodicity plots to preprocessing report.

        This addresses GitHub Issue #6

        Squashed commit of the following:

        commit 2fbaaf44d82fa55e0523bd8e34a6c7d2b978c249
        Author: Brandon Malone <bmmalone@gmail.com>
        Date:   Sun Jul 3 22:03:35 2016 +0200

            Added ORF type periodicity to preprocessing report

        commit 730bcdf48b1ca2e2bb1c726ff2e3ff41d3d68422
        Author: Brandon Malone <bmmalone@gmail.com>
        Date:   Sun Jul 3 21:10:43 2016 +0200

            Added filter to quickly find ORFs which meet minimum profile sum criterion

        commit 4392329abfde3218b1e1a5a0a6c60d7a26af2926
        Author: Brandon Malone <bmmalone@gmail.com>
        Date:   Sun Jul 3 18:34:45 2016 +0200

            Updated ORF type metagene profiles to limit the required number of profiles

        commit dcc09da8571faa342fb2829d3d1b463400c7d46a
        Author: Brandon Malone <bmmalone@gmail.com>
        Date:   Sun Jul 3 17:50:50 2016 +0200

            Fixed indexing error causing latex compilation error

    commit 2fbaaf44d82fa55e0523bd8e34a6c7d2b978c249
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 3 22:03:35 2016 +0200

        Added ORF type periodicity to preprocessing report

    commit 730bcdf48b1ca2e2bb1c726ff2e3ff41d3d68422
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 3 21:10:43 2016 +0200

        Added filter to quickly find ORFs which meet minimum profile sum criterion

    commit 4392329abfde3218b1e1a5a0a6c60d7a26af2926
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 3 18:34:45 2016 +0200

        Updated ORF type metagene profiles to limit the required number of profiles

    commit dcc09da8571faa342fb2829d3d1b463400c7d46a
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 3 17:50:50 2016 +0200

        Fixed indexing error causing latex compilation error

    commit 35fc0dcbe317af09d264a887353773f1e4e2bfc2
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 3 17:40:43 2016 +0200

        Fixed indexing error causing latex compilation error

    commit 85aa2d495bde4d13f45c74300947c3da290ea2d0
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 3 17:34:03 2016 +0200

        Added vim swp files to ignore list

    commit 0e25fbe4f19303ef3f660138ecbdd61e9843584d
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sun Jul 3 13:48:56 2016 +0200

        Added strands to ORF type pie chart.

        This addresses GitHub Issue #12.

    commit 6c41c624053e073a843348b5fc9d1e2b3951a2c4
    Merge: adb2cac a701616
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Jul 2 15:27:45 2016 +0200

        Merge branch 'create-predictions-report' into dev

    commit a7016161508076c0685a1aa6b8c7193eccb7dcbe
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Jul 2 15:27:00 2016 +0200

        Updated report to use agg backend for mpl

    commit adb2cac2a9ec812418598472955783d7352b7cb0
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Sat Jul 2 12:25:21 2016 +0200

        Updated merge-orfs to write gzipped mtx files

    commit 21ef26ae3f102c54808f156679aed2320beaa830
    Merge: 3cdc3c7 bd5acff
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 18:48:19 2016 +0200

        Merge branch 'rpchi-unsmoothed' into dev

        This merge completes Issue #3.

    commit bd5acff151f9ac494a1a4f5e5c820d223ab58399
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 18:47:53 2016 +0200

        Updated documents to explain that rpchi does not use smoothing

    commit 896726e28696417c9d7ff07d13352829e418b313
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 18:35:24 2016 +0200

        Updated predictions report to use unsmoothed profiles for rp-chi

    commit 2729ed5a4f4ad8932174e03171dc47722dca846c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 18:33:46 2016 +0200

        Fixed error message when no ORFs of a given type are present

    commit 3cdc3c70ac417c6b1fa2da77444c9bf504379550
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 16:19:13 2016 +0200

        Updated the rp-chi predictions to use the unsmoothed profiles.

        This addresses the implementation work for GitHub Issue #3.

    commit 4b939bb2af03b8d513469a57bd4f2bac9fce166b
    Merge: 85364bd 3780c77
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 15:16:34 2016 +0200

        Merge branch 'dev' of github.com:dieterich-lab/rp-bp into dev

    commit 3780c773109305aa9c7e24c9e3a8df1bb09eeb2c
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 15:00:36 2016 +0200

        The ORF profiles are gzipped before being written to disk.

        This addresses Redmine Feature #112.

    commit 85364bd0e6b8f7c458fea2d930e50fae0839a23f
    Merge: 8246756 38da983
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:14:09 2016 +0200

        Merge branch 'hotfix-reverse-strand-off-by-one' into dev

        This hotfix addresses github issue #5

    commit 38da98399498cd21b600f820e18c3dabe2f95889
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:13:10 2016 +0200

        Added patch to fix off-by-one error.

        It is unclear how stable this is, though, so metagene profiles by type diagnostics need to be used in the future to ensure we do not continue to see strand-specific biases.

    commit 8246756932043593167f6def151fc671c5ab6c7c
    Merge: d4ea23f a232b2b
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:06:35 2016 +0200

        These merges partially address the predictions report, Redmine Feature #121

        Merge branch 'create-predictions-report' into dev

    commit a232b2bb5db6fff9a018333e3e0cf6632c9a1d14
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 14:05:05 2016 +0200

        Added strand-specific metagene profiles

    commit c1d32e680a9ddc7bd1d46f9d73d6aeccec518a70
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Fri Jul 1 10:14:49 2016 +0200

        Added paths to metagene profile notebook

    commit 6a21f44bceb9e1843587b24e5784d1d1cc94631f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 18:34:20 2016 +0200

        Shifted all negative strand P-sites forward (i.e., back, in relation to the ORFs) by one

    commit e016ac7663606b3bbed538cb9bc670b98e314073
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 18:28:04 2016 +0200

        Updated metagene profile notebook with an example checking strands

    commit 71e28ef5671fd979a95a402123f2f85c7807b25e
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 16:24:41 2016 +0200

        Added script to create ORF predictions analysis figures

    commit 4c23bba5fb6e77149249bb94abef3d98a663ca78
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 16:24:13 2016 +0200

        Added counts to orf type metagene profiles

    commit 60da14f65a6159cce854d5232c5eae1c910b6002
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 14:33:09 2016 +0200

        Added grouping option to length distribution script

    commit e5ebc82534353295fade941f3359869f80e37a1f
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Thu Jun 30 13:38:29 2016 +0200

        Added predictions report script to setup

    commit cf6d172e4842d51f5ce793e51383c992deaebffc
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jun 29 19:49:31 2016 +0200

        Added scripts to visualize orf types and lengths

    commit b1775aa69586c5fa6aca94e3ab61525effc380e8
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jun 29 16:02:13 2016 +0200

        Added orf type visualization script to setup

    commit 76d12e2c1fb2ca393e91ddc5c27da70ad372c599
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jun 29 16:01:04 2016 +0200

        Added script for orf type metagene profiles

    commit 13bc0e95362d70ba4552dbd2893a64fceeed5486
    Author: Brandon Malone <bmmalone@gmail.com>
    Date:   Wed Jun 29 16:00:41 2016 +0200

        Added notebook for orf type metagene profiles

dieterich-lab/rp-bp