066da80a3d
Added KEEP_UNCONDTIONAL option which permits even sites with only filtered records to be included as unfiltered sites in the output
2012-01-19 18:19:58 -05:00
7f3ad25b01
Adding a mode to VariantFiltration to invalidate previously-applied filters to allow complete re-filtering of a VCF.
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T2D VQSR: re-calling now done with appropriate quality settings and using BAQ.
2012-01-19 10:54:48 -05:00
7e082c7750
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-19 09:11:23 -05:00
39e6df5aa9
Fix edge case for very small VCFs
2012-01-19 00:51:28 -05:00
1e037a0ecf
Ensure second-to-last line printed
2012-01-19 00:33:08 -05:00
9946853039
Remove duplicated line
2012-01-19 00:25:22 -05:00
cf9b1d350a
Some minor changes to in-process functions that nobody else uses. CGL now properly ignores no-calls for external VCFs.
2012-01-19 00:20:49 -05:00
ab8f499bc3
Annotate with FS even for filtered sites
2012-01-18 22:04:51 -05:00
b123416c4c
Resolve stale merge changes
2012-01-18 20:56:36 -05:00
2eb45340e1
Initial, raw, mostly untested version of new pool caller that also does allele discovery. Still needs debugging/refining. Main modification is that there is a new operation mode, set by argument -ALLELE_DISCOVERY_MODE, which if true will determine optimal alt allele at each computable site and will compute AC distribution on it. Current implementation is not working yet if there's more than one pool and it will only output biallelic sites, no functionality for true multi-allelics yet
2012-01-18 20:54:10 -05:00
0133d1a901
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-18 09:53:42 -05:00
0268da7560
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-18 09:53:00 -05:00
60024e0d7b
updating TDT integration test
2012-01-18 09:52:50 -05:00
b7c65cb089
Merged bug fix from Stable into Unstable
2012-01-18 09:52:47 -05:00
11982b5a34
We no longer calculate the population-level TDT statistic if there are fewer than 5 trios with full genotype likelihood information. When there is a high degree of missingness the results are skewed or in the worst case come out as NaN.
2012-01-18 09:42:41 -05:00
763c81d520
No longer enforce MAX_ALLELE_SIZE in VCF codec
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-- Instead issue a warning when a large (>1MB) record is encountered
-- Optimized ref.getBytes()[i] => (byte)ref.charAt(i), which avoids an implicit O(n) allocation each iteration through computeReverseClipping()
2012-01-18 07:35:11 -05:00
0c7865fdb5
UnitTest for reverseAlleleClipping
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-- No code modified yet, just implementing a unit test to ensure correctness of the existing code
2012-01-18 07:35:11 -05:00
d5199db8ec
Be explicit about setting the snpEff -onlyCoding option in the pipeline
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When run without an explicit -onlyCoding option, as we've been doing up to
now, snpEff automatically sets -onlyCoding to "true" provided that there is
at least one transcript marked as "protein_coding", which will always be the
case for us in practice (and indeed, all pipeline runs so far with snpEff
2.0.5 have run with -onlyCoding auto-set to "true").
However, given the disastrous effect on annotation quality setting
"-onlyCoding false" has, we wish to be explicit with this option
rather than relying on snpEff's auto-detection logic.
2012-01-17 20:04:27 -05:00
62801e430a
Bugfix for unnecessary optimization
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-- don't cache the ref bytes
2012-01-17 16:40:26 -05:00
f2b0575dee
Detect unreasonably large allele strings (>2^16) and throw an error
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-- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places.
-- Tribble was updated so we actually could read the line properly (rev. to 51 here).
-- Still the parsing algorithms in the GATK aren't happy with such a long allele. Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.
2012-01-17 16:40:26 -05:00
8b0ddf0aaf
Adding notes to CountCovariates docs about using interval lists as database of known variation
2012-01-17 16:13:13 -05:00
56761297dd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-17 15:03:32 -05:00
75f87db468
Replacing Mills file with new gold standard indel set in the resource bundle for release with v1.5
2012-01-17 15:02:45 -05:00
40ebc17437
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-17 14:49:17 -05:00
41d70abe4e
At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.
2012-01-17 14:47:53 -05:00
ae259f81cc
Bug fixing for merging of read fragments when one fragment contained an indel
2012-01-17 14:39:27 -05:00
cde224746f
Bait Redesign supports baits that overlap, by picking only the start of intervals.
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CalibrateGenotypeLikelihoods supports using an external VCF as input for genotype likelihoods. Currently can be a per-sample VCF, but has un-implemented methods for allowing a read-group VCF to be used.
Removed the old constrained genotyping code from UGE -- the trellis calculated is exactly the same as that done in the MLE AC estimate; so we should just re-use that one.
2012-01-17 13:51:05 -05:00
8e23c98dd9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-17 13:46:28 -05:00
32ccde374b
Merged bug fix from Stable into Unstable
2012-01-17 11:08:35 -05:00
3ba918aff1
Error message cleanup in BAM indexing code.
2012-01-17 11:05:42 -05:00
cec7107762
Better location for the downsampling of reads in PrintReads
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* using the filter() instead of map() makes for a cleaner walker.
* renaming the unit tests to make more sense with the other unit and integration tests
2012-01-14 14:06:09 -05:00
b06074d6e7
Updated SortingVCFWriterBase to use PriorityBlockingQueue so that the class is thread-safe
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-- Uses PriorityBlockingQueue instead of PriorityQueue
-- synchronized keywords added to all key functions that modify internal state
Note that this hasn't been tested extensivesly. Based on report:
http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic
2012-01-13 09:33:16 -05:00
28aa353501
Added "unbiased" downsampling parameter to PrintReads
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* also cleaned up and updated part of the unit tests for print reads. Needs a more thorough cleaning.
2012-01-12 16:33:55 -05:00
2c3176eb80
Merged bug fix from Stable into Unstable
2012-01-12 13:31:10 -05:00
cd43f016ce
Fixed NPE in getNextOverlappingBAMScheduleEntry() when mixed mapped/unmapped interval lists are used. Added integrationtest to verify behavior.
2012-01-12 13:29:11 -05:00
ed34b4f088
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-12 10:27:26 -05:00
e7fe9910f7
Create the temp storage for calculating cell values just once as per Mark's TODO
2012-01-12 10:27:10 -05:00
f5f5ed5dcd
Don't initialize the cell conformation values (use an else in the loop instead) as per Mark's TODO
2012-01-12 08:50:03 -05:00
410a340ef5
Swapping the iteration order to run over AF conformations and then samples instead of the reverse minimizes calls to HashMap.get; instead of it being O(n) since we called it for each sample it's now O(1). Runtime on T2D GENES test set is reduced by 5-10%. More optimizations to follow.
2012-01-12 02:04:03 -05:00
77a03c9709
Patching special case in the adaptor clipping
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* if the adaptor boundary is more than MAXIMUM_ADAPTOR_SIZE bases away from the read, then let's not clip anything and consider the fragment to be undetermined for this read pair.
* updated md5's accordingly
2012-01-11 17:47:44 -05:00
aae61767c6
queueJobReport now compresses PDF when running R 2.13+.
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Updated PostCallingQC.scala's VE and R to include missense to silent ratio and plot.
2012-01-10 17:32:30 -05:00
a9a6516527
Merged bug fix from Stable into Unstable
2012-01-10 16:16:10 -05:00
ef50e77ee2
When running Queue jobs locally, merge the stderr to the stdout log if the error file is NOT specified.
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Updated VE strats in the HSP for plotting Ka/Ks by AC.
2012-01-10 16:10:25 -05:00
3475bfafd3
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-10 12:39:15 -05:00
5bf960deb8
adding dbsnp to indel VQSR
2012-01-10 12:38:49 -05:00
25d0d53d88
Moving the approximate summing of log10 vals to MathUtils; keeping the more efficient implementation of fast rounding.
2012-01-10 12:38:47 -05:00
589397d611
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-10 12:36:48 -05:00
c5320ef1af
Resolving changes in integration test during merge
2012-01-10 12:14:16 -05:00
e923a2e512
Revving Picard to incorporate final version of ReadWalker performance improvements.
2012-01-10 12:12:33 -05:00
0f36f6947e
Resolving merge conflicts
2012-01-10 11:44:16 -05:00
Menachem Fromer
Christopher Hartl
Ryan Poplin
Eric Banks
Guillermo del Angel
David Roazen
Mark DePristo
Matt Hanna
Mauricio Carneiro
Khalid Shakir