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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mauricio Carneiro 80d92e0c63 Allowing the GATK to have non-required outputs 
Modified the SAMFileWriterArgumentTypeDescriptor to accept output bam files that are null if they're not required (in the @Output annotation).

This change enables the nWayOut parameter for the IndeRealigner and ReduceReads to operate optionally while maintaining the original single way out.

[#DEV-10 transition:31 resolution:1]
 		2012-10-15 13:49:08 -04:00
..
CNV BCF2 with support symbolic alleles 2012-06-30 11:22:48 -04:00
annotator Update MD5s with new FS score 2012-08-28 08:06:47 -04:00
beagle Fixing remaining integration test errors. Adding missing ex2.bcf 2012-06-30 16:23:11 -04:00
bqsr Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table. 2012-09-20 14:14:34 -04:00
coverage number of stashed changes are lurking in here. In order of importance: 2012-08-21 07:08:58 -04:00
diagnostics Fixing remaining integration test errors. Adding missing ex2.bcf 2012-06-30 16:23:11 -04:00
diffengine Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
fasta Several more walkers have been brought up to use the new Allele representation. 2012-07-27 02:14:25 -04:00
filters Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR 2012-07-25 08:56:39 -04:00
genotyper Increasing the precision of MathUtils.approximateLog10SumLog10 from 1E-3 to 1E-4. Genotyper integration tests change as a result. Expanding the unit tests of MathUtils.log10sumLog10. 2012-10-15 13:24:32 -04:00
indels Allowing the GATK to have non-required outputs 2012-10-15 13:49:08 -04:00
phasing - Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE 2012-07-17 15:21:10 -04:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
validation Allele refactoring checkpoint #3: all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this. 2012-07-27 15:48:40 -04:00
varianteval In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC. 2012-08-14 15:02:30 -04:00
variantrecalibration Update md5s for VQSR, as VQSLOD is now a double and gets the standard double precision treatment in VCF 2012-08-30 19:41:49 -04:00
variantutils Finalizing IndependentAllelesDiploidExactAFCalc 2012-10-15 08:21:03 -04:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
FlagStatIntegrationTest.java Adding integration test for Flag Stat 2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig 2012-09-05 21:10:03 -04:00
PrintReadsIntegrationTest.java ReadShard are no longer allowed to span multiple contigs 2012-08-30 10:15:11 -04:00
PrintReadsUnitTest.java Removed the "Walker" suffix from all walkers that had it. 2012-07-20 17:27:11 -04:00