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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mauricio Carneiro ec475a46b1 Fixing @PG tag uniqueness issue 
The Problem:
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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:
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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:
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* 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:
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http://gsabamboo.broadinstitute.org/browse/GSAUNSTABLE-PARALLEL31

Issue Tracker:
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[fixes 47100885]
 		2013-03-30 20:31:33 -04:00
..
R R issue in Queue fixed. 2013-01-28 14:42:20 -05:00
activeregion Changing CALLED_IN_DB_UNKNOWN_STATUS to count as TRUE_POSITIVEs in the simplified stats for AssessNA12878. 2013-03-14 14:44:18 -04:00
analysis Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
baq Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -05:00
classloader Added verbose error message to the PluginManager 2013-02-19 16:00:35 -05:00
clipping Fixed reported bug in BQSR for RNA seq alignments with Ns. 2013-03-14 11:26:52 -04:00
codecs Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
collections Replace uses of NestedHashMap with NestedIntegerArray. 2013-02-27 14:03:39 -05:00
crypt Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
duplicates Cleanup and unit tests for QualityUtils 2013-02-16 07:31:37 -08:00
exceptions Created new DeprecatedToolChecks class 2013-03-20 06:46:02 -04:00
fasta Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
file Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fragments New GATKSAMRecord concept of a strandless read, update to FS 2013-03-13 11:16:36 -04:00
genotyper PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now 2013-03-26 14:27:13 -04:00
haplotypeBAMWriter PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now 2013-03-26 14:27:13 -04:00
help Created ListAnnotations utility (extends CommandLineProgram) 2013-03-20 06:15:27 -04:00
instrumentation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
interval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
io Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
locusiterator Vast improvements to AssessNA12878 code and functionality 2013-02-21 20:43:12 -05:00
nanoScheduler Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pairhmm Merged bug fix from Stable into Unstable 2013-03-18 12:36:21 -04:00
pileup Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
progressmeter Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter 2013-02-04 15:47:30 -05:00
recalibration The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior. 2013-01-28 15:56:33 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam Fixing @PG tag uniqueness issue 2013-03-30 20:31:33 -04:00
text Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
threading Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variant Upgrades and changes to LeftAlignVariants, motivated by 1000G consensus indel production: 2013-03-29 10:02:06 -04:00
wiggle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
AutoFormattingTime.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
BaseUtils.java - Added more comprehensive tests for consensus creation to RR. Still need to add tests for I/D ops. 2013-02-01 15:37:19 -05:00
BitSetUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ContigComparator.java Generalize and fixup ContigComparator 2013-02-09 09:52:13 -05:00
DeprecatedToolChecks.java Created new DeprecatedToolChecks class 2013-03-20 06:46:02 -04:00
GenomeLoc.java Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -05:00
GenomeLocParser.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
GenomeLocSortedSet.java Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
Haplotype.java HaplotypeCaller now has the ability to only consider the best N haplotypes for genotyping 2013-03-20 22:54:36 -04:00
HasGenomeLocation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
HeapSizeMonitor.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
IndelUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
LRUCache.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MRUCachingSAMSequenceDictionary.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
MannWhitneyU.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
MathUtils.java Rarely-occurring logic bugfix for GenotypeConcordance, streamlining and testing of MathUtils 2013-03-28 23:25:28 -04:00
Median.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MendelianViolation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MultiThreadedErrorTracker.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NGSPlatform.java Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests 2013-02-09 11:16:21 -05:00
PathUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtils.java Relax bounds checking in QualityUtils.boundQual 2013-02-22 08:46:59 -05:00
SWPairwiseAlignment.java Expanded functionality for writing BAMs from HaplotypeCaller 2013-03-03 12:07:29 -05:00
SWPairwiseAlignmentMain.java Expanded functionality for writing BAMs from HaplotypeCaller 2013-03-03 12:07:29 -05:00
SampleUtils.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
SequenceDictionaryUtils.java Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -05:00
SimpleTimer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
UnvalidatingGenomeLoc.java Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc. 2013-01-30 10:45:29 -05:00
Utils.java Fixing @PG tag uniqueness issue 2013-03-30 20:31:33 -04:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00