404ef741f1
Merged bug fix from Stable into Unstable
2011-10-13 18:02:06 -04:00
2ebdff074c
Update MD5s for SOLiD recalibration
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-- MD5 db had spelling error; fixed
-- Bug in AlignmentUtils resulted in some bases not being color space corrected. The integration test caught the change, and it's clear that the new version is correct, as the prev. version was not considering the last the N qualities for reads with a ND operation.
2011-10-13 18:01:51 -04:00
5a881360df
Merged bug fix from Stable into Unstable
2011-10-13 15:54:43 -04:00
7cab6f6bb0
Bug fixes for thread unsafe simple timer and bad Ns treatment in AlignmentUtils
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-- SimpleTimer is now threadsafe using synchronized method keywords
-- Bug fix for alignmentToByteArray() where the N case was refPos++ not the now correct refPos += elementLength
2011-10-13 15:53:12 -04:00
9aecd50473
Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it.
2011-10-12 15:44:54 -04:00
e53a952aeb
Added ION Torrent support to CountCovariates.
2011-10-12 01:57:02 -04:00
a2733a451f
Added NotCalled feature to GAV
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Added "not called" and "no status" to the truth table. Very useful.
2011-10-11 19:31:45 -04:00
ae83420637
Merged bug fix from Stable into Unstable
2011-10-11 12:26:08 -04:00
794f275871
SnpEff is now marked as a RodRequiringAnnotation instead of an ExperimentalAnnotation.
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Having SnpEff grouped with the Experimental annotations was proving problematic, since it
requires a rod. Placing it in its own group should improve the situation somewhat, making it
easier to request "all annotations except for SnpEff".
2011-10-11 12:08:56 -04:00
cfd0ac8410
Merged bug fix from Stable into Unstable
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Conflicts:
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
2011-10-11 12:03:51 -04:00
24b72334b3
UnifiedGenotyper now correctly initializes the VariantAnnotator engine.
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This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.
Added an integration test to cover this case so that it doesn't break again.
2011-10-11 12:02:05 -04:00
0429b38021
Merged bug fix from Stable into Unstable
2011-10-11 11:19:38 -04:00
1c485d8b5e
Forgot that no matter how trivial a change it's a good idea to compile first
2011-10-11 11:18:41 -04:00
6418f4d69b
Merged bug fix from Stable into Unstable
2011-10-11 11:13:18 -04:00
1975de1b32
Second try: hide --do_indel_quality in AnalyzeCovariates
2011-10-11 11:11:29 -04:00
6506ea83e8
Revert "Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users"... a hidden passenger change made it through.
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This reverts commit 70e10ccb1be90dcff8f4485ae6ee036db2d1ac86.
2011-10-11 11:03:12 -04:00
4c1d8c8d44
Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users
2011-10-11 11:01:06 -04:00
cffc959e58
Moving to archive instead, since no one owns it
2011-10-10 23:55:57 -04:00
77c983c5b5
No one claimed this walker and it doesn't have integration tests or GATKdocs so it doesn't belong in public.
2011-10-10 15:17:54 -04:00
fb72bcf732
DiffObjects no longer prints out the file name in the status so MD5 are stable
2011-10-10 15:10:57 -04:00
ac41b303fd
Merge branch 'vcfAlleles'
2011-10-10 13:23:52 -04:00
0c0a619b08
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-10 13:23:40 -04:00
b1124b2b61
Trivial Qscript to evaluate the impact of max deletion fraction in UG
2011-10-10 13:22:59 -04:00
e3ff4f4266
Failing MD5 because output now contains absolute path
2011-10-10 11:05:02 -04:00
3e6c16d961
CombineVariants preserves allele order
2011-10-10 11:04:38 -04:00
a4bb842958
RankSum tests have lightly different MD5 results based on allele order
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-- UG GENOTYPE_GIVEN_ALLELES now uses the order of alleles in the VCF, so this changes the MD5
2011-10-10 11:04:07 -04:00
46e7370128
this.allele, getAlleles(), and getAltAlleles() now return List not set
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-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
2011-10-09 11:45:55 -07:00
822654b119
UnitTests for allele getting functions in VC in prep for move from set to list
2011-10-09 10:36:14 -07:00
e19dba86a6
Merged bug fix from Stable into Unstable
2011-10-08 22:37:12 -04:00
0016c707a3
Codecs other than VCF accidentally bled into vcf.jar. Unfortunately, vcf.jar
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turned out to be the *only* home for these other codecs. This change pushes
them back into StingUtils.jar.
2011-10-08 22:24:35 -04:00
c67f6c076b
simpleMerge now preserves allele order
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-- UnitTests for dangerous PL merging cases in the multi-allelic case. The new behavior is correct
2011-10-08 17:39:53 -07:00
e94e6ba101
A UnitTest to ensure that the order of alleles is maintained
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-> A, C, T and A, T, C are different and must be maintained. The constructors were doing this appropriately, so nothing needed to be changed
2011-10-08 08:47:58 -07:00
ff3dccd062
Fixing errors in queueJobReport runtime unit
2011-10-07 12:04:53 -07:00
ec14a4a606
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-07 08:38:50 -07:00
6fbd41724a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-07 11:20:00 -04:00
4514bc350f
More reliable way of finding the Tribble jar.
2011-10-07 11:19:29 -04:00
181c76750e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 22:38:55 -04:00
ca9cd9b688
Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC.
2011-10-06 22:38:44 -04:00
f91b015e0e
Made the BaseTest.testDir absolute
2011-10-06 22:33:21 -04:00
c7864c7256
Filter application order is now deterministic, in the order defined by the walker
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-- For no apparent reason we were using a HashSet to store the ReadFilters, so the order of operations was really arbitrarily applied. The order now is
(1) the order of the walker intrinsic filters
(2) read group black list (if provided)
(3) command line filters (if provided)
2011-10-06 18:51:40 -07:00
0b88af4af9
Counts of records failing filters are displayed sorted
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-- Stops random ordering of the output, as the counts are returned sorted by string name of the class
-- Deleted now unused sh*tty assessors in Utils
2011-10-06 18:42:26 -07:00
d1e70d6ec2
Removed Nx counting of reads in metrics with -nt > 1
2011-10-06 18:29:26 -07:00
d367945dec
Extending InsertSizeDistribution to compute stats by sample and by read group
2011-10-06 15:14:17 -07:00
c61804a450
Rename the long version of the argument name to more accurately reflect its purpose.
2011-10-06 16:14:04 -04:00
61a3dfae24
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 15:58:04 -04:00
6eb87bf58a
RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop.
2011-10-06 15:57:49 -04:00
6d9c210460
Updating MD5s for updated BAM with read groups
2011-10-06 12:15:48 -07:00
c528233578
Now uses exampleBAM and exampleFASTA instead of the misc. copies in validation_data
2011-10-06 12:03:45 -07:00
ab357ef900
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 10:50:02 -07:00
1b0735f0a3
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 13:41:45 -04:00
Mark DePristo
Eric Banks
Mauricio Carneiro
David Roazen
Guillermo del Angel
Matt Hanna
Khalid Shakir