c8b1c92a6c
Updating the other half of the PPP
2011-12-12 10:55:41 -05:00
13905c00b3
Updating PacbioProcessingPipeline to new Queue standards
2011-12-09 16:51:02 -05:00
1bfe28067f
Don't try to genotype an indel even bigger than the reference window size, or else we'll be out of bounds. Necessary to handle Phase 1 integrated callset with large deletions. Better error indication when validating a GenomeLoc.
2011-12-08 12:54:08 -05:00
cb284eebde
Further updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 14:00:57 -05:00
447e9bff9e
Updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 09:57:45 -05:00
75d93e6335
Another corner condition fix: skip likelihood computation in case we cut so many bases there's no haplotype or read left
2011-11-22 22:46:12 -05:00
32a77a8a56
Prevent out of bound error in case read span > reference context + indel length. Can happen in RNAseq reads with long N CIGAR operators in the middle.
2011-11-22 13:57:24 -05:00
c62082ba1b
Making this class public again as per request from Cancer folks
2011-11-18 12:34:27 -05:00
6a5d5e7ac9
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-11-16 09:57:13 -05:00
7ac5cf8430
Getting rid of unsupported CountReadPairs walker in stable. Removal of
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remainder of pairs processing framework to follow in unstable.
2011-11-16 09:53:59 -05:00
348f2db7fd
Fix for HMM optimization. If the two penalty arrays match exactly the function should return the end of the array instead of 0.
2011-11-09 22:00:52 -05:00
d828eba7f4
Allow comments in a table-formatted file to precede the header line.
2011-11-09 15:27:38 -05:00
11abb4f9d1
Better error message.
2011-11-09 11:25:28 -05:00
d3a533b82e
Revert "a"
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This reverts commit 1175f50ddbf389f5da74d27dc725596582ae15af.
2011-11-09 11:22:26 -05:00
5eaf800281
a
2011-11-09 11:22:20 -05:00
091229e4db
MVLikelihoodRatio now checks if the family string is provided before attempting to instantiate. Also check that variant contexts have both genotypes and genotype likelihoods.
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Table codec now yells at users for not providing a HEADER with the table - parsing tables without a header line was causing the first line of the file to be eaten.
Table feature now has a toString method.
These are minor bug fixes.
2011-11-09 11:03:29 -05:00
b0e6afec48
Bug fix for HMM optimization. Need to also check the gap continuation penalty array for the index with the first discrepancy.
2011-11-08 14:51:25 -05:00
0b181be61f
Bug fix in SelectVariants when using a discordance track but no sample specifications. Added integration test to test this.
2011-11-07 15:25:16 -05:00
6297561326
Adding the new jar
2011-11-07 15:08:19 -05:00
86312a956a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-11-07 14:59:49 -05:00
2d1e385ca4
Adding note to VQSR docs about Rscript being needed in the environment PATH.
2011-11-07 14:04:13 -05:00
aa0c8c3600
Revving Tribble jar to v40. Our last jar was busted.
2011-11-07 11:30:08 -05:00
cdd40d1222
Removing contracts for the SimpleTimer
2011-11-06 22:22:49 -05:00
90a053ea93
Don't change the mapping quality of MQ=255 reads in IR
2011-11-05 22:40:45 -04:00
de07e06cbc
Merge remote-tracking branch 'unstable/master'
2011-11-04 15:57:13 -04:00
e99871f587
Bug fix for decode loc
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-- decodeLoc() wasn't skipping input header lines, so the system blew up when there was an = line being split.
2011-11-04 13:20:54 -04:00
a340a1aeac
Bug fix. decodeLoc() should update lineNo so you get meaningful line no when indexing
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due to malformed VCF files.
2011-11-04 11:44:24 -04:00
849c0757f2
Bug fix for LocusScatterFunction when no intervals are provided
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-- Now correctly grabs reference contigs and cuts them all up, rather than NPE as intervalString == null.
2011-11-04 10:55:09 -04:00
9f260c0dc1
Zero byte index bug fix for RandomlySplitVariants + cleanup
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-- vcfWriter2 was never being closed in onTraversalDone(), so the on the fly index file was being created but never actually properly written to the file.
-- This bug is ultimately due to the inability of the GATK to allow multiple VCF output writers as @Output arguments, though
-- Removed the unnecessary local variable iFraction, = 1000 * the input fraction argument. Now the system just uses a double random number and compares to the input fraction at all. Is there some subtle reason I don't appreciate for this programming construct?
2011-11-04 09:45:20 -04:00
5a47c3c8a0
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-04 09:36:42 -04:00
020b8b88ef
GATKSAMRecord refactor in the tools
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No tools should create SAMRecords internally. This commit should move all internals of the current tools to GATKSAMRecord.
2011-11-03 17:33:42 -04:00
e89ff063fc
GATKSAMRecord refactor
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The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...).
* No tools should create SAMRecord anymore, use GATKSAMRecord instead *
2011-11-03 15:43:26 -04:00
f1df6c0c81
Misc cleanup in haplotype caller after incorporating Mark's FragmentCollection to merge overlapping read pairs.
2011-11-03 13:51:19 -04:00
748f8f1edc
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-03 10:06:48 -04:00
c7f51e92a0
Mostly working version of multi-sample analysis qscript
2011-11-02 23:00:17 -04:00
e8bceb1eaa
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-02 21:13:54 -04:00
78a00d2ddc
Updating UG integration tests (needed updating only because the -mbq default is different from the old -mmq one).
2011-11-02 21:13:44 -04:00
52b16bf739
Must check whether there's a normal vs. extended pileup before asking for it.
2011-11-02 20:45:24 -04:00
e1edd6bd12
Removing the min mapping quality argument since it wasn't being used in the normal processing of the pileups in UG - only for indel pileups. Instead, we apply the min base quality to the reads in the pileup for indels and define it to be the min 'confidence' of the base. Docs are updated but I didn't rename the argument as I don't want people to complain.
2011-11-02 20:32:58 -04:00
c22a14ee3b
Merged bug fix from Stable into Unstable
2011-11-02 17:53:56 -04:00
e4a583a53f
Fixing docs: No -I in this walker
2011-11-02 17:53:32 -04:00
e94fcf537b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-02 16:29:19 -04:00
4d35272916
Bug fixes with Mauricio to functions in ReadUtils used by reduced reads and the haplotype caller.
2011-11-02 16:29:10 -04:00
8a2929c1dd
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-02 16:21:00 -04:00
e2f40da27f
Scala script to run multi-sample analysis
2011-11-02 16:20:57 -04:00
bd977c2d92
Bug fix to avoid infinite loop in GATKScatterFunction
2011-11-02 16:20:42 -04:00
967ff647b8
Reduced reads shouldn't contribute to Fisher Strand calculations
2011-11-02 13:07:20 -04:00
cf0e699226
QualByDepth was inefficiently iterating over the pileup 2 times for some reason. Removed non-useful annotation classes.
2011-11-02 12:58:38 -04:00
4501dce58d
Fixing merge conflict
2011-11-02 12:50:32 -04:00
54331b44e9
New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths.
2011-11-02 12:47:30 -04:00
Mauricio Carneiro
Guillermo del Angel
Ryan Poplin
Eric Banks
Matt Hanna
Christopher Hartl
Mark DePristo