0d53e184a7
Mapping quality name change.
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The mapping quality of the consensus reads is the average of the RMS of all reads that contributed to the consensus, weighted according to the size of the contribution of each read.
2011-09-23 12:16:09 -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
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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
Mauricio Carneiro
Mark DePristo
Eric Banks
Matt Hanna
Christopher Hartl
Ryan Poplin
Christopher Hartl