96ffc63caa
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-23 12:57:04 -04:00
e3d4efb283
Remove N2 EXACT model code, which should never be used
2011-09-23 11:55:21 -04:00
fb6ac127a1
Merged bug fix from Stable into Unstable
2011-09-23 10:56:58 -04:00
bcecc61715
Fixing md5 because file changed on disk
2011-09-23 10:56:16 -04:00
27ce3c822e
Merge branch 'stable'
2011-09-23 09:04:52 -04:00
2bb77a7978
Docs for all VariantAnnotator annotations
2011-09-23 09:04:16 -04:00
68d5544ec9
Accurate docs for IOCrusher
2011-09-23 09:03:50 -04:00
dd65ba5bae
@Hidden for DocumentationTest and GATKDocsExample
2011-09-23 09:03:37 -04:00
dfce301beb
Looks for @Hidden annotation on all classes and excludes them from the docs
2011-09-23 09:03:04 -04:00
106a26c42d
Minor file cleanup
2011-09-23 08:25:20 -04:00
a9f073fa68
Genotype merging unit tests for simpleMerge
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-- Remaining TODOs are all for GdA
2011-09-23 08:24:49 -04:00
4397ce8653
Moved removePLs to VariantContextUtils
2011-09-23 08:24:20 -04:00
054c475416
Updating md5 because the file changed
2011-09-23 07:49:59 -04:00
a8e0fb26ea
Updating md5 because the file changed
2011-09-23 07:33:20 -04:00
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
...
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:
...
- 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
Mark DePristo
Eric Banks
Mauricio Carneiro
Matt Hanna
Christopher Hartl
Ryan Poplin
Christopher Hartl