0111505ea9
Terrible. Swapping the paternal and sample ids.
2012-02-02 11:41:16 -05:00
0c562756eb
Add a memory limit so this thing doesn't get killed on the farm
2012-02-02 10:30:09 -05:00
45bf2562cc
.
2012-02-02 09:11:17 -05:00
f8c5406084
Add the ability to extract samples
2012-02-02 09:06:39 -05:00
b567ed8793
Use the right reference path :(
2012-02-01 12:35:18 -05:00
87a63d54d6
fix the script!
2012-02-01 12:05:29 -05:00
810996cfca
Introducing: VariantsToPed, the world's most annoying walker! And also a busted QScript to run it that I need Khalid's help debugging ( frownie face ). Note that VariantsToPed and PlinkSeq generate the same binary file (up to strand flips...thanks PlinkSeq), so I know it's working properly. Hooray!
2012-02-01 10:39:03 -05:00
25d943f706
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-01 10:32:11 -05:00
056b24ccd6
Resolving merge conflicts with LocusIteratorByState
2012-01-31 16:13:32 -05:00
febc634557
Changing PileupElement's isSoftClipped to isNextToSoftClip since soft clipped bases aren't actually added to pileups, oops. Removing the intrinsic clustered variants filter from the HaplotypeCaller
2012-01-31 16:06:14 -05:00
7f70612beb
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-31 11:59:25 -05:00
a630db1703
Oops...HierarchicalMicroScheduler was transforming any exception from the walker level into a ReviewedStingException.
...
Thanks to Ryan for pointing this out.
2012-01-31 11:58:21 -05:00
faba3dd530
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-31 10:25:29 -05:00
17dbe9a95d
A few cleanups in the LocusIteratorByState
...
* No more N's in the extended event pileups
* Only add to the pileup MQ0 counter if the read actually goes into the pileup
2012-01-31 09:40:51 -05:00
f9162ea705
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-30 19:45:19 -05:00
abb91cf26b
Increasing the size of the active regions that are produced by the active probability integrator, more context is needed to call more complex events
2012-01-30 15:36:12 -05:00
d5d4fa8a88
Fixed discordance bug reported by Brad Chapman
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discordance now reports discordance between genotypes as well (just like concordance)
2012-01-30 09:50:45 -05:00
3164c8dee5
S3 upload now directly creates the XML report in memory and puts that in S3
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-- This is a partial fix for the problem with uploading S3 logs reported by Mauricio. There the problem is that the java.io.tmpdir is not accessible (network just hangs). Because of that the s3 upload fails because the underlying system uses tmpdir for caching, etc. As far as I can tell there's no way around this bug -- you cannot overload the java.io.tmpdir programmatically and even if I could what value would we use? The only solution seems to me is to detect that tmpdir is hanging (how?!) and fail with a meaningful error.
2012-01-29 15:14:58 -05:00
0e17cbbce9
Merged bug fix from Stable into Unstable
2012-01-27 16:03:16 -05:00
a9671b73ca
Fix to permit proper handling of mapping qualities between 128 to 255 (which get converted to byte values of -128 to -1)
2012-01-27 16:01:30 -05:00
f7ac1f4a69
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-27 15:12:55 -05:00
fc08235ff3
Bug fix in active region traversal, locusView.getNext() skips over pileups with zero coverage but still need to count them in the active probability integrator
2012-01-27 15:12:37 -05:00
052a4bdb9c
Turning off PHONE HOME option in the MDCP
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* MDCP is for internal use and there is no need to report to the Amazon cloud.
* Reporting to ASW_S3 is not allowing jobs to finish, this is probably a bug.
2012-01-27 11:13:30 -05:00
0f2e8400b5
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-27 10:12:50 -05:00
ec9920b04f
Updating the SAM TAG for Original Alignment Start to "OP"
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per Mark's recommendation to reuse the Indel Realigner tag that made it to the SAM spec. The Alignment end tag is still "OE" as there is no official tag to reuse.
2012-01-27 08:51:39 -05:00
13d1626f51
Minor improvements in ref QC walker. Unfortunately this doesn't actually catch Chris's error
2012-01-27 08:24:22 -05:00
2a565ebf90
embarrassing fix-up, thanks Khalid.
2012-01-26 19:58:42 -05:00
246e085ec9
Unit tests for GATKSAMRecord class
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* new unit tests for the alignment shift properties of reduce reads
* moved unit tests from ReadUtils that were actually testing GATKSAMRecord, not any of the ReadUtils to it.
* cleaned up ReadUtilsUnitTest
2012-01-26 17:06:36 -05:00
0d4027104f
Reduced reads are now aware of their original alignments
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* Added annotations for reads that had been soft clipped prior to being reduced so that we can later recuperate their original alignments (start and end).
* Tags keep the alignment shifts, not real alignment, for better compression
* Tags are defined in the GATKSAMRecord
* GATKSAMRecord has new functionality to retrieve original alignment start of all reads (trimmed or not) -- getOriginalAlignmentStart() and getOriginalAligmentEnd()
* Updated ReduceReads MD5s accordingly
2012-01-26 17:06:36 -05:00
07f72516ae
Unsupported platform should be a user error
2012-01-26 16:14:25 -05:00
cdff23269d
HaplotypeCaller now uses insertions and softclipped bases as possible triggers. LocusIteratorByState tags pileup elements with the required info to make this calculation efficient. The days of the extended event pileup are coming to a close.
2012-01-26 15:56:33 -05:00
673ceadd11
While this fix worked for the evaluator module, it could potentially have bad effects in the phasing walkers. Special-case nocalls in the PhasingEvaluator and return AllelePair to previous state.
2012-01-26 13:06:36 -05:00
9c6fda7e15
Yup. I was right.
2012-01-26 12:54:11 -05:00
7d059540a4
Allow segments of genome to be excluded in generating a reference panel. Occasionally targets would contain no variation (typically, in the middle of the centromere), which beagle doesn't particularly like, and errors out rather than producing empty output files. The best way to deal with these is to just exclude the regions on a second-pass, and the remaining bits will be gathered with no additional work.
...
AllelePair is being mean and not telling me what genotype it sees when it finds a non-diploid genotype, but i suspect it's a no-call (".") rather than a no call ("./.").
2012-01-26 12:43:52 -05:00
25532bdc37
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 11:43:32 -05:00
390d493049
Updating ActiveRegionWalker interface to output a probability of active status instead of a boolean. Integrator runs a band-pass filter over this probability to produce actual active regions. First version of HaplotypeCaller which decides for itself where to trigger and assembles those regions.
2012-01-26 11:37:08 -05:00
859dd882c9
Don't make it standard for now
2012-01-26 00:38:16 -05:00
c5e81be978
Adding pairwise AF table. Not polished at all, but usable none-the-less.
2012-01-26 00:37:06 -05:00
702a2d768f
Initial version of multi-allelic summary module in VariantEval
2012-01-25 19:42:55 -05:00
9a60887567
Lost an import in the merge
2012-01-25 19:41:41 -05:00
cba5f1a8b1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-25 19:19:03 -05:00
ddaf51a50f
Updated one integration test for indels
2012-01-25 19:18:51 -05:00
add6918f32
Cleaner, more efficient way of determining the last dependent set in the queue.
2012-01-25 16:21:10 -05:00
db645a94ca
Added options to make the batch-merger more all-inclusive: keep all indels, SNPs (even filtered ones) but maintain their annotations. Also, VariantContextUtils.simpleMerge can now merge variants of all types using the Hidden non-default enum MultipleAllelesMergeType=MIX_TYPES
2012-01-25 16:10:59 -05:00
ef335a5812
Better implementation of the fix; PL index is now traversed in order.
2012-01-25 15:15:42 -05:00
8e2d372ab0
Use remove instead of setting the value to null
2012-01-25 14:41:34 -05:00
05816955aa
It was possible that we'd clean up a matrix column too early when a dependent column aborted early (with not enough probability mass) because we weren't being smart about the order in which we created dependencies. Fixed.
2012-01-25 14:28:21 -05:00
2799a1b686
Catch exception for bad type and throw as a TribbleException
2012-01-25 12:15:51 -05:00
96b62daff3
Minor tweak to the warning message.
2012-01-25 11:55:33 -05:00
fb863dc6a7
Warn user when trying to run with EMIT_ALL_SITES with indels; better docs for that option.
2012-01-25 11:50:12 -05:00
Christopher Hartl
Ryan Poplin
Matt Hanna
Mauricio Carneiro
Mark DePristo
Menachem Fromer
Eric Banks