07dbf0bd40
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 13:39:24 -05:00
26762d6c6f
Folding recent HMM changes into Haplotype Caller. Misc bug fixes throughout HC.
2011-11-10 13:36:03 -05:00
39678b6a20
Check for reads with missing read groups and throw a UserException when encountered. Mauricio said this wouldn't break integration tests.
2011-11-10 13:34:45 -05:00
9490d71bc8
Folding recent HMM changes into Haplotype Caller. Misc bug fixes throughout HC.
2011-11-10 13:26:29 -05:00
0d8983feee
outputting the RG information
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setReadGroup now sets the read group attribute for the GATKSAMRecord
2011-11-09 23:35:00 -05:00
315ac68b0b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 22:37:36 -05:00
6313aae2c4
Adding checks for hasBasePileup() before calling getBasePileup() as per GS thread
2011-11-09 22:37:26 -05:00
74a18d3de8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-09 22:29:40 -05:00
24712c0221
Merged bug fix from Stable into Unstable
2011-11-09 22:28:27 -05:00
8942406aa2
Use MathUtils to compare doubles instead of testing for equality
2011-11-09 22:05:21 -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
9a4486a9e6
BaseCounts now include N's
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Fixing unit tests accordingly.
2011-11-09 21:29:33 -05:00
82bf09edf3
Mark Standard Annotations with an asterisk
2011-11-09 20:42:31 -05:00
04b122be29
Fix for bug reported on GetSatisfaction
2011-11-09 20:33:36 -05:00
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
3afbd0e526
Sliding Window Header now includes filtered data information
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This is a necessary framework for the filtered data consensus reads to be produced.
2011-11-09 20:16:22 -05:00
6ee90ada14
Quick optimization to the SlidingWindow builder
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from O(n^2) to O(n). Not bad.
2011-11-09 20:16:21 -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
8e519e7d5d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-08 16:07:12 -05:00
c49efcf631
Two small improvements to ValidationSiteSelector: a) add argument to ignore genotypes, and make sure selection works in sites-only VCF (in which case we can't select for polymorphism in samples), b) add ability to include filtered sites if requested
2011-11-08 16:06:18 -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
66ad2b941c
Merged bug fix from Stable into Unstable
2011-11-07 15:08:30 -05:00
6297561326
Adding the new jar
2011-11-07 15:08:19 -05:00
41f296ee6d
Merged bug fix from Stable into Unstable
2011-11-07 15:00:25 -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
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
bb448b27d2
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-07 13:26:37 -05:00
63eeb5a56c
MultiSampleCalling script update
2011-11-07 13:23:34 -05:00
759f4fe6b8
Moving unclaimed walker with bad integration test to archive
2011-11-07 13:16:38 -05:00
aa0c8c3600
Revving Tribble jar to v40. Our last jar was busted.
2011-11-07 11:30:08 -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
Ryan Poplin
Eric Banks
Mauricio Carneiro
Christopher Hartl
Guillermo del Angel
Mark DePristo