taoliu/MACS — pull request #7 by benjschiller (2012-02-01 02:43:39+00:00)
Title: change to bam reader

previous method broke the SAM/BAM definition and didn't properly read paired-end data aligned with bowtie. Taking the rightmost read also isn't possible when only one read is aligned (so it unnecessarily discards a lot of data)

Note: This broken in earlier versions of MACS too. I've been using a patched version.