RefCov v0.3 provides critical fixes and several new features. Fixes include restoring several modules that were absent in the previous release. New features include: 1) cluster-coverage for detecting contiguous clusters of sequence reads across a reference, 2) the ability to evaluate coverage of entire chromosomes using the BAM file header as the region-of-interest, ex. --roi-file-path=$BAM --roi-file-format=bam, 3) normalization of coverage using a defined Perl-compatible equation, 4) relative coverage based on a defined list of size bins, and 5) optional output of the chromosome start and end as BED-style columns.
May 23, 2012