New logic for assigning reads to reference genomes using new AlignmentReader class and setting new uniquely and preferentially aligned counts/mismatch rates; now uses commons-logging instead of slf4j for logging, replaced deprecated GnuParser with DefaultParser from commons-cli, updated date in copyright notice.
New logic for assigning reads to reference genomes using new AlignmentReader class and setting new uniquely and preferentially aligned counts/mismatch rates; now uses commons-logging instead of slf4j for logging, replaced deprecated GnuParser with DefaultParser from commons-cli, updated date in copyright notice.

crukci-bioinformatics/MGA