samtools merge to trace transformations applied to @RG IDs

[SamStudio8]

Adds a -t <FILE> option for samtools merge to create a tab-delimited text file in the format;

bam_filename    @RG_ID    Transformed_@RG_ID

eg.

/dat/test_input_1_b.bam fish PG:llama   fish PG:llama
/dat/test_input_1_b.bam cow cow
/dat/test_input_1_b.bam colt    colt
/dat/test_input_1_c.bam fish    fish
/dat/test_input_1_c.bam cow cow-55424A4
/dat/test_input_1_c.bam colt    colt-3A2CCEF5
/dat/test_input_1_a.bam fish    fish-4861F4EF
/dat/test_input_1_a.bam cow cow-39E5EF
/dat/test_input_1_a.bam colt    colt-1802EEEC

This allows users to keep track of a particular read group ID through the merge process via a simple lookup file. For testing purposes I have hijacked the third merge test in test.pl and performed a diff between the resulting trace file and a provided expected trace file (above). Note that the test relies on a system call to sed to remove the unknown user-specific path to the /dat/ files before the comparison.

(I am unsure whether the fish PG:llama RG ID is intentional, the tab delimiter appears to be missing from the input BAM in question.)

[SamStudio8]

Does merge offer this option now?

[valeriuo]

No. And it seems -t has been used for tag sorting, in the meantime.
merge needs some rework, as there are quite a few old PRs that address it. Also, it could make better use of the new header API.