adds sample names and read-group (RG) tags to BAM alignments
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bamtools @ 6111130 updated bamtools May 26, 2012
.gitmodules initial commit Apr 28, 2011
Makefile remove unnecessary -static flag May 25, 2011
README updated README Apr 28, 2011
bamaddrg.cpp resolve failure of index file open May 24, 2012


bamaddrg: adds read groups to input BAM files, streams BAM output on stdout.

This is intended for use "fixing up" RG tags on the fly so that they reflect
the source file from which the aligment originated from.  This allows the
"safe" merging of many files from many individuals into one stream, suitable
for input into downstream processing systems such as freebayes (a population
variant detector).


To tag multiple files simultaneously, use as such:

    % bamaddrg -b file1.bam -s jill -r group.s1.1 \
               -b file2.bam -s jill -r group.s1.2 \
               -b file3.bam -s bill \
               -b file4.bam \
       | freebayes ...

This would add the sample name "jill" to records from file1.bam and file2.bam,
while specifying that specific read group identify alignments from each file.
Alignments from file3.bam would be tagged with sample name "bill" and read
group id "bill", and samples from file4.bam would be tagged with sample name
"file4.bam" and read group id "file4.bam."