aacec3aeb0
rod for binary GELI files (still needs to be tested)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1198 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:25:56 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
d8fbb2b62c
Refactoring; make a better home for the MalformedReadFilteringIterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1194 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:54:20 +00:00
4ba2194b5e
Filter reads whose alignment starts past the end of the contig to which it allegedly aligns.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1188 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 22:27:44 +00:00
5d7393d7cb
Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1183 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 15:18:05 +00:00
5735c87581
Basic infrastructure for filtering malformed reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1178 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 22:50:22 +00:00
31313481f6
Temporary patch to filter out bad alignments that aren't quite fully reported as bad.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1176 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 18:41:55 +00:00
d19366eaad
Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1173 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 15:41:30 +00:00
4019cd2bd7
Added ROD for parsing hapmap3 genotype files.
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Tweak to TabularROD to allow HapMapGenotypeROD to work.
Added HapMapGenotypeROD to list of RODs in ReferenceOrderedData.java.
Modified MultiSampleCaller to return a single object with most of the relvant information.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1169 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 16:28:24 +00:00
e5e249d4ac
temporary fix to deal with screwy SOLiD reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1168 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-05 03:25:57 +00:00
cf1854b339
Fix for monsterous problems with solid data -- now can dynamically expand recalibration tables on the fly as reads declare additional read groups -- use assumeFaultyHeader flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1167 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 17:15:49 +00:00
bcda66d2db
Simple performance improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1166 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 16:45:23 +00:00
0d00823332
Fix for performance bug in extending the read with X's in cases where the read is aligned off the end of the contig.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1165 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-03 16:17:38 +00:00
62807139fc
Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:54:01 +00:00
1c83b4d949
forgot to take out some test code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1157 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:18:37 +00:00
bc17ff567a
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:15:50 +00:00
47cb9f169e
Stable tool that's the reverse of merging -- splits a file into individual BAM files, one for each sample ID in the SAM header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1155 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 12:56:46 +00:00
bb92eb8b1c
added a fix for overlapping reads in the locus context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1153 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 02:08:59 +00:00
9b182e3063
Prep for documenting command-line arguments: delete some arguments that don't make sense any more given
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the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:23:35 +00:00
d58eeb7539
Don't cry wolf: only one warning is now emitted, instead of tons of warnings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1139 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 13:50:37 +00:00
a3e0ec20c4
Kill the TraverseByLocusWindows traversal. TraverseLocusWindows will take its place.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1138 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 13:46:35 +00:00
e93f751bd7
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 21:59:54 +00:00
f5cba5a6bb
Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:17:24 +00:00
9fca79ed62
Read groups are now sorted in the output data, for convenience
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1129 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:50:44 +00:00
03f8177a53
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:51:55 +00:00
7ecc43e9a7
Fixed subtle null ptr exception discovered by Kiran. Now deals with the rare situation where you have only say Q28 bases at dbSNP sites, so you fail in the Table recalibration step with a null pointer error into the data structure indexed by quality score. If you are Q score above those seen before you aren't modified in any way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1118 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 18:57:42 +00:00
95e2ae0171
Deal with reads whose ends are aligned off the end of a chromosome.
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Includes update to ignore non-ATCG bases (not just 'N')
(Also, create a BWA dir for future work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1117 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:50:05 +00:00
65a788f18a
Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls.
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Some doodling around with indel calling in an EM context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1116 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:32:12 +00:00
d7d4298917
Some files to support generic genotype outputing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1112 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 15:43:41 +00:00
491ed70b44
TraverseByLocusWindow -- asstd bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:51:38 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
ad3a3aa350
First pass at passing lists of files / lists of interval arguments work. Note that the interval
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ROD system will throw up its hands and not deal with intervals at all if multiple interval files
are passed in (see JIRA GSA-95).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:44:23 +00:00
83816fb801
Stop using the annoying refIterator (temp change until new traversal is green lighted)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1103 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:05:39 +00:00
0d9041380d
remove printouts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1100 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:54:14 +00:00
102b38c055
Sketch of new version of TraverseByLocusWindow, and a flag to conditionally turn it on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1097 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:20:56 +00:00
5b1c23a7f2
changes to fix and test the interval based traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:54:15 +00:00
347608cfe0
remove hacked traversal in preparation for move to Matt's new one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1091 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 14:32:05 +00:00
0a50f2e160
Updated and near final version of tabular recalibration system. Uses 'yates' correction for low-occupancy quality bins. Faster and more robust handling of input and output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1082 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 03:52:12 +00:00
ef546868bf
Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.
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Desperately needs cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-23 23:48:06 +00:00
8b4d0412ca
Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1072 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 21:11:18 +00:00
bcb64d92e9
Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
26eb362f52
Added novel / known split to variant eval. That is, emits all of the standard analyses on SNP partitioned into those known in the provided known db and those novel. Also fixed problem with counting bases within subsets
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1068 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 21:27:40 +00:00
d3f0c51944
longer update times so we don't overwhelm when running genome-wide
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1067 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-21 14:10:02 +00:00
9e26550b0d
Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-20 16:00:23 +00:00
dde52e33eb
Cleanup of the cleaned read injector based on Eric's feedback.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1062 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 22:04:47 +00:00
8ac40e8e2d
Updated version of the recalibration tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
d748c85dc4
Cleaned code and reorganized -- moving in the right direction for v2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1052 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 22:28:34 +00:00
1bca144119
Moving things around
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1049 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:06:46 +00:00
3c40db260d
Added REFERENCE_BASES required annotation for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:03:57 +00:00
7a921c908c
Can now adjust the genotype likelihoods of a variant returned from the rod. This automatically causes the lodBtr, lodBtnb, and genotype to be recomputed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1041 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 07:26:37 +00:00
ebanks
hanna
jmaguire
depristo
aaron
kiran