c49cc623de
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-22 17:26:21 -04:00
dab7232e9a
simpleMerge UnitTest for not annotating and annotating to different info key
2011-09-22 17:26:11 -04:00
30ab3af0c8
A few more simpleMerge UnitTest tests for filtered vcs
2011-09-22 17:14:59 -04:00
5cf82f9236
simpleMerge UnitTest tests filtered VC merging
2011-09-22 17:05:12 -04:00
46ca33dc04
TestDataProvider now can be named
2011-09-22 17:04:32 -04:00
96c875399c
Merging many bug fixes to reduce reads
2011-09-22 17:04:11 -04:00
f1f7335e7b
In the trim to 95% curation function, ensure that no filtering happens when the sd is zero (e.g. when BAD_CYCLES is uniformly zero across all relevant samples).
2011-09-22 16:46:38 -04:00
4040d1c7d6
More conservative defaults for reduce reads
2011-09-22 15:53:23 -04:00
39b54211d0
Fixed hard clipping soft clipped bases after hard clips
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if soft clipped bases were after a hard clipped section of the read, the hard clip was clipping the left soft clip tail as if it were a right tail. Mayhem.
2011-09-22 15:46:55 -04:00
5bca1f732f
Little bug fixes in preQC:
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- Filter out per-library information in per-sample metrics so that our aggregator doesn't crash out
while we figure out how to handle data per-library rather than per-sample.
- Compare preQC metrics for custom captures to all exome data. Note that not every metric makes sense
when compared to every other bait set, so a warning message is emitted on the summary page.
2011-09-22 15:18:40 -04:00
68da555932
UnitTest for simpleMerge for alleles
2011-09-22 15:16:37 -04:00
1acf7945c5
Fixed hard clipped cigar and alignment start
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* Hard clipped Cigar now includes all insertions that were hard clipped and not the deletions.
* The alignment start is now recalculated according to the new hard clipped cigar representation
2011-09-22 14:51:14 -04:00
80d7300de4
Unit test was passing in FORMAT as one of the sample names. There used to be a hack in the VCFHeader to check for this and remove it and I couldn't figure out why, but now I know. Hack was removed and now the unit test passes in only the sample names as per the contract.
2011-09-22 13:28:42 -04:00
4e9020c9f7
Fixed alignment start for hard clipping insertions
2011-09-22 13:28:25 -04:00
9c1728416c
Revert "Updating md5 for fixed file" because this was fixed properly in unstable (but will break SnpEff if put into Stable).
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This reverts commit 6b4182c6ab3e214da4c73bc6f3687ac6d1c0b72c.
2011-09-22 13:16:42 -04:00
888d8697b1
Merged bug fix from Stable into Unstable
2011-09-22 13:16:31 -04:00
15a410b24b
Updating md5 for fixed file
2011-09-22 13:15:41 -04:00
8811bb8668
Merge branch 'stable'
2011-09-22 12:11:01 -04:00
ba5f83fee2
start of VariantContextUtils UnitTest
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-- 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
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-- 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!
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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)
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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
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-- 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).
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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.
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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
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-- 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
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-- 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
Mark DePristo
Mauricio Carneiro
Matt Hanna
Eric Banks
Christopher Hartl
Ryan Poplin
Christopher Hartl