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gatk-3.8/java/test/org/broadinstitute/sting/gatk/walkers
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chartl 480859db50 Contractified version of MannWhitneyU. Some behavior has been changed: 
- Running a test when there are no observations of at least one of the sets now breaks the MWU contract
   + MWU returns Pair(Double.NaN,Double.NaN) in these instances to maintain the contract of never returning null
   + No more Double.Infinity values will appear
 - RankSumTests now probe the return values for NaNs, and don't annotate if they appear
 - For small sets where the probability is calculated recursively, the z-value is now the inversion of the error function
    and not the approximate z-value
 - UG and Annotator integration tests updated to reflect changes



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5845 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-05-23 13:57:15 +00:00
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annotator Contractified version of MannWhitneyU. Some behavior has been changed: 2011-05-23 13:57:15 +00:00
beagle PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only. 2011-05-11 12:07:44 +00:00
coverage -ct x no longer includes coverage in the previous bin 2011-02-24 15:52:04 +00:00
fasta Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
filters PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only. 2011-05-11 12:07:44 +00:00
genotyper Contractified version of MannWhitneyU. Some behavior has been changed: 2011-05-23 13:57:15 +00:00
indels Fix for IndelRealigner memory problem. Now the Constrained mate fixing writer is told whether a read has been modified and, if it wasn't, can dump it when the cache needs to get flushed at places with tons of coverage. 2011-05-06 19:34:41 +00:00
phasing Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test. 2010-12-08 17:22:29 +00:00
qc Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this. 2011-05-20 15:43:27 +00:00
recalibration PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only. 2011-05-11 12:07:44 +00:00
sequenom continuing from last night, the integration tests weren't covering the right behavior either 2011-04-28 13:30:57 +00:00
varianteval PLEASE READ ME! In order to prepare for the upcoming changes to VCF4, we felt it was best to split up the vcf3 and vcf4 codecs (vcf4 is not backwards compatible to vcf3 and certain changes are too complex to handle in both codecs). Using the 'VCF' rod type in the GATK will now throw a UserException for vcf3.2 or vcf3.3 files telling you to use the 'VCF3' type instead (and vice versa). Integration/unit tests have been updated. For programmers: note that there is currently a lot of code duplication in the two codecs (although I pulled out the easy stuff to a VCFCodecUtils class); however WE ARE FREEZING THE VCF3 CODEC AND WILL NO LONGER MAKE CHANGES TO IT. All updates/improvements will be targetted to the vcf4 codec only as vcf3 is there only to be able to read legacy files. People should really be using vcf4 files only. 2011-05-11 12:07:44 +00:00
variantrecalibration Ensuring a minimum number of variants when clustering with bad variants. Better error message when Matrix library fails to calculate inverse. 2011-05-12 01:48:37 +00:00
variantutils Significant change to the way subsetting by sample works with monomorphic sites. Now keeps the alt allele, even if a record is AC=0 after the subset. Previously, the system dropped the alt allele, which I don't think is the right behavior. If you really want a VCF without monomorphic sites, use the option to drop monomorphic sites after subsetting. See detailed information below. 2011-05-21 13:59:16 +00:00
BAQIntegrationTest.java Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails. 2011-01-28 15:08:21 +00:00
ClipReadsWalkersIntegrationTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
PileupWalkerIntegrationTest.java Updated to now longer include 2nd-best base output 2011-04-03 20:13:10 +00:00
PrintReadsIntegrationTest.java --simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on. 2011-03-26 14:57:18 +00:00
PrintReadsWalkerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00