89a581a66f
Added ability to specify arguments in files via -args/--arg_file
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Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()
2011-10-24 15:58:34 -04:00
f6ccac889b
Merged bug fix from Stable into Unstable
2011-10-23 16:37:12 -04:00
585a45b7a3
Bug fix for ClipReadsWalker when stats output isn't provided
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-- See http://getsatisfaction.com/gsa/topics/clipreadswalker?utm_content=topic_link&utm_medium=email&utm_source=reply_notification
2011-10-23 16:36:48 -04:00
c3cb07fc1d
Relocating the ReduceBAM script.
2011-10-22 13:35:52 -04:00
4913f8a60f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-21 17:45:07 -04:00
86305a5dcf
Adjusting the memory limits of the MDCP
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Indel caller needs more than 3G for large datasets.
2011-10-21 17:41:52 -04:00
102dafdcbc
Validation of GATKSamRecord in read filters
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Moved the validation of the GATKSamRecord to the MalformedReadFilter with the intent to make the read filter the ultimate validation location for sam records. This way we can opt to filter out malformed reads if we know what we are doing or blow up otherwise.
2011-10-21 17:40:43 -04:00
f4b409fa0d
CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result
2011-10-21 14:07:20 -04:00
9f867d77ca
no sort order
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subtle bug fixed.
2011-10-20 18:44:09 -04:00
c9d8b22092
Added BWASW support to the pipeline
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Data Processing Pipeline can now use BWASW for realigning the reads. Useful for Ion Torrent data.
2011-10-20 18:36:28 -04:00
093cd95c5d
Merged bug fix from Stable into Unstable
2011-10-20 17:03:22 -04:00
d7367c152a
Fixing 'revert' when not realigning
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RevertSam was reverting the alignment information and that was screwing up the pipeline if you didn't want to run it with BWA. Fixed.
2011-10-20 17:01:54 -04:00
558a7a81f0
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-20 16:23:32 -04:00
ed402588cc
Adding the "gold standard NA12878" target
2011-10-20 16:19:13 -04:00
6f72b3de6a
Forgot to add this in too (oops)
2011-10-19 18:46:31 -04:00
cd8a6d62bb
You know how the wiki has a big section on commiting local changes to BRANCHES of the repository you clone it from? Yeah. It sucks if you don't do that.
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This commit contains:
- IntronLossGenotyper is brought into its current incarnation
- A couple of simple new filters (ReadName is super useful for debugging, MateUnmapped is useful for selecting out reads that may have a relevant unaligned mate)
- RFA now matches my current local repository. It's in flux since I'm transitioning to the new traversal type.
+ the triggering read stash pilot required me to change the scope of some of the variables in the ReadClipping code, private -> protected. Those are all the changes there.
- MendelianViolation restored to its former glory (and an annotator module that uses the likelihood calculation has been added)
+ use this rather than a hard GQ threshold if you're doing MV analyses.
- Some miscellaneous QScripts
2011-10-19 17:42:37 -04:00
d8d73fe4f2
Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown.
2011-10-19 15:11:13 -04:00
5a6468c11e
Allowing ./X genotypes and adding a unit test to ensure that this case is covered from now on (especially given that we may want to revert in the future). Reverting this change is really easy and entails uncommenting a few lines of code. But for now, despite Mark's objections, this case is allowed in the VCF spec and we are wrong not to allow it.
2011-10-19 11:52:05 -04:00
48c4a8cb33
Make error messages clearer (even I was confused)
2011-10-19 11:49:16 -04:00
6cadaa84c9
Just use validate() from super class since it does the same thing
2011-10-19 11:48:23 -04:00
d79b57d6f4
Fixing cases where the Object equals function wasn't being properly overridden in the haplotype caller classes.
2011-10-19 08:57:38 -04:00
c27e2fb676
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-18 15:23:05 -04:00
2125c4f38f
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-18 14:49:00 -04:00
e5fc828546
With Khalid's implicit approval, I have removed this line that overrides the memory limit of the VCF-gathering function, so that the inherited limit remains
2011-10-18 14:47:39 -04:00
f77f2eeb7d
Fix for new ID structure
2011-10-18 13:04:43 -04:00
1a92ee3593
No longer adds a binding of ID -> . when the ID field is dot in the VCF
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-- Really we should make ID a primary key in VariantContext. Putting it into the attributes is just annoying now
2011-10-18 10:57:02 -04:00
e5b793f4ce
A VCFToPED writer for bridging VCF files to Haploview
2011-10-18 10:55:46 -04:00
e45fcb66eb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-17 15:56:19 -04:00
1e6794c539
fixing typo in VariantsToTable docs
2011-10-17 15:56:02 -04:00
92e1cbfb6c
Updating docs and adding option to use a very large file for GATK vs. Tribble comparison
2011-10-17 15:52:41 -04:00
0de8550f17
Merged bug fix from Stable into Unstable
2011-10-17 15:29:53 -04:00
c1329c4dde
Fixing a binary to logical or
2011-10-17 15:29:45 -04:00
9e4963efc8
Merged bug fix from Stable into Unstable
2011-10-17 15:27:38 -04:00
ec911ce5bb
Even better error messages
2011-10-17 15:27:22 -04:00
d065bf1715
Merged bug fix from Stable into Unstable
2011-10-17 15:25:47 -04:00
a7cf9cdc67
Fixing error message typo
2011-10-17 15:25:35 -04:00
589df6b7cf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-17 14:35:14 -04:00
6b02354d84
Adding a new getter in VariantsToTable to extract the indel event length.
2011-10-17 14:34:52 -04:00
3550798c4c
Merged bug fix from Stable into Unstable
2011-10-17 13:58:56 -04:00
4108a294f7
Better error message when a RodBinding file doesn't exist
2011-10-17 13:58:46 -04:00
cc76826f78
Merged bug fix from Stable into Unstable
2011-10-17 13:38:11 -04:00
09a09cacef
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-10-17 13:38:00 -04:00
fd4540cd32
Fixed extraordinarily subtle race condition with contracts invariant
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-- all of the methods in the class must be synchronized or the internal state can be inconsistent with the contract invariant when entering the class in a non-synchronized method, even when that method doesn't care about the object's internal state
2011-10-17 13:37:55 -04:00
2193da6bfb
Merged bug fix from Stable into Unstable
2011-10-16 07:37:20 -04:00
dcd4eee15f
Revert "Intentionally breaking the binary release as a test."
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The test was successful -- the packaging error was detected and
prevented from propagating out into the binary/source releases.
This reverts commit 8f2a1462d94ce50fb7c1b1d0c40142b109e9c38e.
2011-10-16 07:24:33 -04:00
88c9a35b2a
Merged bug fix from Stable into Unstable
2011-10-15 20:28:48 -04:00
46badee76a
Intentionally breaking the binary release as a test.
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This is to test the ability of the new release system
to detect the kinds of packaging errors we couldn't
detect before (in this case, missing codecs). If all goes
as expected, "GSA-Stable: Release" will fail, preventing
the binary release and github from getting updated, while
"GSA-Stable: All Tests" and all of the other old test plans
will pass.
Will revert this in a bit -- if the system works as it should,
our users will never see it until after it's been reverted.
2011-10-15 20:20:41 -04:00
900eb19acb
Merged bug fix from Stable into Unstable
2011-10-14 23:05:01 -04:00
c756da1798
Remove unnecessary debugger port listening from GATKDoclet invocation.
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This caused a race condition between concurrently-running bamboo plans.
2011-10-14 22:59:12 -04:00
88d6b8bc1f
Merged bug fix from Stable into Unstable
2011-10-14 20:13:38 -04:00
Khalid Shakir
Mark DePristo
Mauricio Carneiro
Guillermo del Angel
Christopher Hartl
Eric Banks
Ryan Poplin
Menachem Fromer
David Roazen