68da555932
UnitTest for simpleMerge for alleles
2011-09-22 15:16:37 -04:00
8811bb8668
Merge branch 'stable'
2011-09-22 12:11:01 -04:00
ba5f83fee2
start of VariantContextUtils UnitTest
...
-- tests rsID merging
2011-09-22 12:10:39 -04:00
5e06a45628
Fix the AnalayzeCovariates packaging.
2011-09-22 11:55:40 -04:00
8ca4b5e938
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-22 11:42:19 -04:00
d3cc25454c
Updating the MDCP
2011-09-22 11:27:40 -04:00
93dd1faa5f
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-22 11:20:10 -04:00
a05c959e5a
Empty unit tests for VariantContextUtils
...
-- will be expanded over the day
2011-09-22 11:20:07 -04:00
3fdee2b9ed
Merge from stable into unstable
2011-09-22 11:19:43 -04:00
623c49765d
NO BAQ ON EXOMES!
...
says the boss.
2011-09-22 11:13:40 -04:00
63758efc17
Adding in a qscript for running the ILG (as calculating the insert size distribution needs to happen first).
2011-09-22 11:02:26 -04:00
4f4a0fc38a
Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git
2011-09-22 11:01:58 -04:00
982c47bfa7
Remove duplicate effort in ReadUtils (with apologies to Mauricio)
...
Big (but not major) cleanup of code in ILG - mostly excising the old likelihood model
Activated the early-abort check for ILG. I think it should be better this way.
2011-09-22 10:58:26 -04:00
c514df6d18
Merge of stable into unstable
2011-09-22 10:34:27 -04:00
f81a41b889
Updating MD5s for CombineVariants
...
-- Old version had broken RSIDs, new version is fixed. No longer see rs1234,. as it is now just rs1234
2011-09-22 10:30:25 -04:00
b8ea9ceb68
Adding integration test that uses the -V:dbsnp binding to make sure it won't fail later on if someone messes with Tribble.
2011-09-21 22:43:31 -04:00
8f8b59a932
My interpretation of the VCF spec is that the FORMAT field should only be present if there is genotype/sample data. So the VCFCodec now throws an exception when it encounters such a case. I had to fix one of the integration test VCFs.
2011-09-21 22:23:28 -04:00
e53cb79d42
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-21 20:26:54 -04:00
5d0f284305
Fixing exome specific arguments to the VQSR in the methods development calling pipeline
2011-09-21 20:26:28 -04:00
dc96f6da79
Merge branch 'master' of ssh://chartl@gsa2/humgen/gsa-scr1/chartl/dev/git
2011-09-21 18:18:41 -04:00
f9cdc119af
Added a method to ReadUtils that converts reads of the form 10S20M10S to 40M (just unclips the soft-clips).
...
Be careful when using this - if you're writing a bam file it will be potentially written out of order (since the previous alignment start was at the M, not the S).
2011-09-21 18:16:42 -04:00
faff6e4019
Failed to commit changes to the GATKReport required for more easy access when using the files as data sources (read: histograms) for walkers
2011-09-21 18:15:23 -04:00
96768c8a18
Sending latest bug fixes to Reduce Reads to the main repository
2011-09-21 17:43:11 -04:00
70335b2b0a
Hard clipping soft clipped reads to fix misalignments.
...
Pre-softclipped reads (with high qual) are a complicated event to deal with in the Reduced Reads environment. I chose to hard clip them out for now and added a todo item to bring them back on in the future, perhaps as a variant region.
2011-09-21 17:12:01 -04:00
1b47dcb1b5
Removing old intron loss genotyper (though all of the development tree got rebased away, I hope); committing a new version of the likelihood calculation model and the genotyper, as well as the sequence simulator (and a QualityScoreHisotgramWalker to help with the simulation of read qualities). RFA will remain local for now.
2011-09-21 16:55:09 -04:00
ef05827c7b
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-21 16:40:47 -04:00
3b51d9106a
Adding in likelihood calculations for mendelian violations. Also fixing a minor and rare bug in SelectVariants when specifying family structure on the command line.
2011-09-21 16:40:29 -04:00
04968c88b3
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-21 15:43:25 -04:00
c6ba944719
Adding bgzip vcf file for unit tests
2011-09-21 15:39:45 -04:00
6bcfce225f
Fix for dynamic type determination for bgzip files
...
-- GZipInputStream handles bgzip files under linux, but not mac
-- Added BlockCompressedInputStream test as well, which works properly on bgzip files
2011-09-21 15:39:19 -04:00
9f6f0c443c
Marginally cleaner isVCFStream() function
...
-- cleanup trying to debug minor bug. Failed to fix the bug, but the code is nicer now
2011-09-21 15:25:01 -04:00
5fef6dc5d0
Merged bug fix from Stable into Unstable
2011-09-21 15:23:06 -04:00
2585fc3d6c
Updating Rscript path doc text for Broad users
2011-09-21 15:22:26 -04:00
74f9ccf6dd
Merge
2011-09-21 11:30:11 -04:00
6592972f82
Putative fix for BAQ array out of bounds
...
-- Old code required qual to be <64, which isn't strictly necessary. Now uses the Picard SAMUtils.MAX_PHRED_SCORE constant
-- Unittest to enforce this behavior
2011-09-21 11:25:08 -04:00
174859fc68
Don't allow whitespace in the INFO field
2011-09-21 11:14:54 -04:00
ecc7f34774
Putative fix for BAQ problem.
2011-09-21 11:09:54 -04:00
7d11f93b82
Final bugfix for CombineVariants
...
-- Now handles multiple records at a site, so that you don't see records like set=dbsnp-dbsnp-dbsnp when combining something with dbsnp
-- Proper handling of ids. If you are merging files with multiple ids for the same record, the ids are merged into a comma separated list
2011-09-21 10:58:32 -04:00
b36d396c16
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-21 10:16:24 -04:00
34f435565c
Accidentally committed unclean tribble jar to repo
2011-09-21 10:16:17 -04:00
a91ac0c5db
Intermediate commit of bugfixes to CombineVariants
2011-09-21 10:15:05 -04:00
ac4f2d6d34
Fixing choppy consensus reads
...
When the consensus read had holes in the middle, the consensus was being finalized but not properly reinitialized. It was restarting with the old coordinates of the finalized consensus, misaligning following bases.
2011-09-21 00:49:50 -04:00
48c413fee8
Now throws an error when the mismatch fraction is too high
2011-09-20 21:28:31 -04:00
3b9314aecf
Max fraction of mismatch test for debugging
...
-- Useful example for individuals who want to compute mismatches between a read and the reference.
2011-09-20 20:42:18 -04:00
b04d8eab55
Merged bug fix from Stable into Unstable
2011-09-20 17:24:14 -04:00
758ecf2d43
Bringing latest updates of ReduceReads to the master repository
2011-09-20 16:35:09 -04:00
d9ea764611
SnpEff annotator now adds OriginalSnpEffVersion and OriginalSnpEffCmd lines to the header of the VCF output file.
...
This change is urgently required for production, which is why it's going into Stable+Unstable
instead of just Unstable.
The keys for the SnpEff version and command header lines in the VCF file output by
VariantAnnotator (OriginalSnpEffVersion and OriginalSnpEffCmd) are intentionally
different from the keys for those same lines in the SnpEff output file (SnpEffVersion
and SnpEffCmd), so that output files from VariantAnnotator won't be confused
with output files from SnpEff itself.
2011-09-20 16:30:55 -04:00
bffd3cca6f
Bug fix for reduced read; only adds regular bases for calculation
...
-- No longer passes on deletions for genotyping
2011-09-20 15:07:06 -04:00
83bb91020f
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-20 14:52:54 -04:00
a97e039a62
Thanks to Chris for instructing me to use VCFExtractIntervals to get proper scattering of Variant Annotation
2011-09-20 14:29:39 -04:00
Mark DePristo
Eric Banks
Mauricio Carneiro
Christopher Hartl
Ryan Poplin
Christopher Hartl
David Roazen
Menachem Fromer