transMap filtering is now performed immediately using PslCDnaFilter.
transMap filtering is now performed immediately using PslCDnaFilter.

A simple awk command is also used to remove long transcripts.

This allows for the FilterTransMap step to simply focus on paralog resolution as well as split gene resolution. This also should hopefully fix problems in the MUSCLE/FastTree step where poor quality alignments lead to MSA failure.

ucsc-mus-strain-cactus/Comparative-Annotation-Toolkit,ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit,ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit