7a46273d75
Consensus reads had filtered data read names
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fixed.
2011-11-10 13:58:31 -05:00
c14b182501
Add reads in the recursive call
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was missing consensus reads that got added from the recursive call. This is was a side-effect of the filtered data implementation. Fixed.
2011-11-10 13:58:31 -05:00
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
18f829f76b
Towards a full G1KPhaseI table creation script
2011-11-10 13:27:54 -05:00
dd1810140f
-stratIntervals is optional
2011-11-10 13:27:32 -05:00
67b022c34b
Cleanup for new SampleUtils function
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-- getVCFHeadersFromRods(rods) is now available so that you don't have getVCFHeadersFromRods(rods, null) throughout the codebase
2011-11-10 13:27:13 -05:00
9490d71bc8
Folding recent HMM changes into Haplotype Caller. Misc bug fixes throughout HC.
2011-11-10 13:26:29 -05:00
35fe9c8a06
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-10 11:11:33 -05:00
714cac21c9
Testdata for IntervalStratification
2011-11-10 11:08:34 -05:00
dc4932f93d
VariantEval module to stratify the variants by whether they overlap an interval set
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The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
-T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to safely use this module you should provide entire contigs worth of variants, and let the interval strat decide overlap, as opposed to using -L which will not properly work with symbolic variants.
Minor improvements to create() interval in GenomeLocParser.
2011-11-10 10:58:40 -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
0111e58d4e
Don't generate PDF unless you have -run specified
2011-11-09 14:45:40 -05:00
29df96a77b
First working version of G1KPhase1SummaryTable.scala
2011-11-09 14:43:53 -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
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
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
Mauricio Carneiro
Ryan Poplin
Eric Banks
Mark DePristo
Christopher Hartl
Guillermo del Angel