d00b2c6599
Adding a synthetic read for filtered data
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* Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data.
* Synthetic reads can now have deletions (but not insertions)
* New reduced read tag for filtered data synthetic reads *(RF)*
* Sliding window header now keeps information of consensus and filtered data
* Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads
2011-11-09 20:16:22 -05:00
21bf43f3bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 15:34:40 -05:00
02d5e3025e
Added integration test for intervals from bed file
2011-11-09 15:34:19 -05:00
85bffe1dca
Merged bug fix from Stable into Unstable
2011-11-09 15:29:14 -05:00
d828eba7f4
Allow comments in a table-formatted file to precede the header line.
2011-11-09 15:27:38 -05:00
8205efbb29
Merge branch 'master' into intervals
2011-11-09 15:27:15 -05:00
d64f8a89a9
Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.
2011-11-09 15:24:29 -05:00
f080f64f99
Preserve RG information on new GATKSAMRecord from SAMRecord
2011-11-09 14:39:20 -05:00
f9530e0768
Clean unnecessary attributes from the read
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this gives on average 40% file size reduction.
2011-11-09 14:39:20 -05:00
9427ada498
Fixing no cigar bug
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empty GATKSAMRecords will have a null cigar. Treat them accordingly.
2011-11-09 14:39:20 -05:00
149b79eaad
Merged bug fix from Stable into Unstable
2011-11-09 11:26:30 -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
5451fbc2b2
Merged bug fix from Stable into Unstable
2011-11-09 11:06:15 -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
e1b4c3968f
Fixing GATKSAMRecord bug
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when constructing a GATKSAMRecord from scratch, we should set "mRestOfBinaryData" to null so the BAMRecord doesn't try to retrieve missing information from the non-existent bam file.
2011-11-08 16:50:36 -05:00
e973ca2010
fixing merge conflict.
2011-11-08 14:55:05 -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
94dc447a70
Merged bug fix from Stable into Unstable
2011-11-07 15:26:35 -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
0534149708
Merged bug fix from Stable into Unstable
2011-11-07 14:07:08 -05:00
2d1e385ca4
Adding note to VQSR docs about Rscript being needed in the environment PATH.
2011-11-07 14:04:13 -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
Mauricio Carneiro
Eric Banks
Christopher Hartl
Ryan Poplin
Mark DePristo