e639f0798e
mergeEvals allows you to treat -eval 1.vcf -eval 2.vcf as a single call set
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-- A bit of code cleanup in VCFUtils
-- VariantEval table to create 1000G Phase I variant summary table
-- First version of 1000G Phase I summary table Qscript
2011-11-09 14:35:50 -05:00
759f4fe6b8
Moving unclaimed walker with bad integration test to archive
2011-11-07 13:16:38 -05:00
c1986b6335
Add notes to the GATKdocs as to when a particular annotation can/cannot be calculated.
2011-11-07 11:06:19 -05:00
724e3f3b0d
Merged bug fix from Stable into Unstable
2011-11-06 22:23:22 -05:00
cdd40d1222
Removing contracts for the SimpleTimer
2011-11-06 22:22:49 -05:00
5c565d28b9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-06 10:26:19 -05:00
3517489a22
Better --sample selection integration test for VE. The previous one would return true even if --sample was not working at all.
2011-11-06 01:07:49 -04:00
1c4e429a1c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-06 00:05:56 -04:00
a12bc63e5c
Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext.
2011-11-05 23:54:28 -04:00
ad57bcd693
Adding integration test to cover using expressions with IDs (-E foo.ID)
2011-11-05 23:53:15 -04:00
90a053ea93
Don't change the mapping quality of MQ=255 reads in IR
2011-11-05 22:40:45 -04:00
611a395783
Now properly extending candidate haplotypes with bases from the reference context instead of filling with padding bases. Functionality in the private Haplotype class is no longer necessary so removing it. No need to have four different Haplotype classes in the GATK.
2011-11-05 12:18:56 -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
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
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
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
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
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
392e0aeace
Moved unit tests into master IntervalUtilsUnitTest
2011-11-02 10:52:00 -04:00
c2b97030a4
IntervalUtils for completely balanced locus-based scatter/gather
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-- scatterLocusIntervals master utility
-- Moved around some general functionality from GenomeLocSortedSet to GenomeLoc
-- Util function for reversing a list (List<T> -> List<T>, unlike Collections version)
-- DoC is PartitionType.INTERVAL
-- Significant unit tests on new functionality (all passing)
-- Ready for real-world testing, as soon as I can get LocusScatterFunction.scala to actually work
2011-11-02 10:49:40 -04:00
5fc613f972
Better default partition types for walkers
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-- Added PartitionType.READ, and associated ReadScatterFunction. ReadScatterFunction is literally just ContigScatterFunction until someone wants to implement something better
-- LocusWalkers (and subclasses RodWalkers and RefWalkers) are by default PartitionType.LOCUS.
2011-11-01 19:47:10 -04:00
36600fd8e9
added MQ of low MQ/BQ to consensus RMS
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Bases that were excluded for MQ and BQ filters are now contributing to the MQ RMS (but not to consensus base counts and variant/not variant region triggers).
2011-11-01 17:46:12 -04:00
b004489c6d
Moving ReduceRead TAG to GATKSAMRecord
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ReduceReads are now a feature of a GATKSAMRecord, so the tag and the special methods needed to use it will now be housed by the GATKSAMRecord.
2011-11-01 17:12:09 -04:00
17cc484dbd
Revert "ReduceReads ref bases are now output as '='
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Reducing the reference bases to '=' results in an extra compression of 13% on average. The GATK is not ready to handle files with '=' bases, and the decision was to implement this a an engine support, not a part of ReduceReads.
2011-11-01 16:35:07 -04:00
0839c75c8d
More minor fixes to docs
2011-10-31 21:49:27 -04:00
74b018a1f3
Minor fixes to docs
2011-10-31 21:41:43 -04:00
31ee5432c5
Merged bug fix from Stable into Unstable
2011-10-31 14:56:59 -04:00
cdde32acbd
Merged bug fix from Stable into Unstable
2011-10-31 14:21:15 -04:00
f62af0291b
Check for invalid VCF records (not enough tokens) instead of assuming they are there.
2011-10-31 14:09:51 -04:00
bed0acaed4
nWayOut now adds PG tag to the header as it should. Also, additional hidden option added: keepPGTags. If invoked, IndelRealigner PG tags from previous runs (if any) are kept in the header and the new PG tag is simply added, instead of overriding them
2011-10-31 12:28:28 -04:00
389380a590
ReduceReads ref bases are now output as '=' to save space
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Restructured the sliding window framework to manipulate a wrapped version of the SAMRecord that contains information about the reference.
2011-10-30 12:04:39 -04:00
0ca7428e76
Allow processing of empty intervals, but warn user when this case is encountered.
2011-10-28 12:12:14 -04:00
649dfe98f0
Add VCF header for any expressions that are requested
2011-10-28 10:22:19 -04:00
8b1a62da27
Adding unit test to cover overlapping intervals from the same source with the intersection rule.
2011-10-28 09:59:43 -04:00
057a79f598
This argument should be annotated as @Input
2011-10-28 09:44:49 -04:00
4ba7c0cecd
Moving to private
2011-10-28 09:29:28 -04:00
1bdd76c2f2
These tools now use the IntervalBinding system to handle intervals instead of doing it all manually
2011-10-28 09:28:12 -04:00
6ba08a103d
Empty ROD files should generate an exception when used for creating intervals. Moved some now obsolete files to the archive as the realigner will now read all target intervals into memory.
2011-10-28 09:23:25 -04:00
3d04bb5608
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-27 23:55:18 -04:00
19e27d4568
Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
2011-10-27 23:55:11 -04:00
cafc245a43
For some reason, a class of Codecs (including TableCodec) require that a GenomeLocParser be passed in to do the position processing. Why can't they just return a Feature with chr, start, stop? Isn't that the right thing?
2011-10-27 23:54:28 -04:00
Mark DePristo
Eric Banks
Ryan Poplin
Mauricio Carneiro
David Roazen
Andrey Sivachenko