Mauricio Carneiro ec475a46b1 Fixing @PG tag uniqueness issue ... The Problem: ------------ the SAM spec does not allow multiple @PG tags with the same id. Our @PG tag writing routines were allowing that to happen with the boolean parameter "keep_all_pg_records". How this fixes it: ------------------ This commit removes that option from all the utility functions and cleans up the code around the classes that used these methods off-spec. Summarized changes: ------------------- * Remove keep_all_pg_records option from setupWriter utility methos in Util * Update all walkers to now replace the last @PG tag of the same walker (if it already exists) * Cleanup NWaySamFileWriter now that it doesn't need to keep track of the keep_all_pg_records variable * Simplify the multiple implementations to setupWriter Bamboo: ------- http://gsabamboo.broadinstitute.org/browse/GSAUNSTABLE-PARALLEL31 Issue Tracker: -------------- [fixes 47100885]		2013-03-30 20:31:33 -04:00
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R	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Fixing @PG tag uniqueness issue	2013-03-30 20:31:33 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00