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
f8f2152f9c
fixing ReduceReads MD5s
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now that we're using OP instead of OS.
2012-01-27 10:53:24 -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
cb04c0bf11
Removing javaassist 3.7, lucene library dependancies
2012-01-27 08:24:22 -05:00
2a565ebf90
embarrassing fix-up, thanks Khalid.
2012-01-26 19:58:42 -05:00
0de6aca29b
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 18:26:41 -05:00
d54e237671
Take advantage of Eric's fix for multiAllelic AC calculation, and also add fix to have the original allele's INFO field be passed through for batch merging
2012-01-26 18:25:30 -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
44c3a41f67
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 13:25:33 -05:00
dbe9eb70fe
Updating HC integration tests after merge
2012-01-26 13:25:22 -05:00
bd27f3bc9b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 12:52:16 -05:00
67c89cadad
Fixes for pool caller to match UG outputs at certain sites: implement min base qual/min mapping qual read filter so those reads are filtered from pileups, and implemented filter for sites that have a too large a fraction of deletions
2012-01-26 12:52:00 -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
9a63a9ae3c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 00:38:25 -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
774e540042
Fixing broken test
2012-01-26 00:31:41 -05:00
5b9c8ab01b
Another quick update missed in the merge
2012-01-25 21:53:20 -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
d405ec2a0d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-25 15:53:32 -05:00
4337dcd7e4
More pool caller bug fixes: the QUAL field was actually multiplied by 10 (accounting for a lot of singletons that shouldn't have been there), and correct AD output
2012-01-25 15:53:03 -05:00
66772d0ebf
Next iteration in the pool caller: more bug fixes, start of big refactoring to clean up interfaces, moved up a lot of attributes that really belonged to a site up from the Pool class, added by default option to filter out a call if there's no reference depth (instead of just skipping the call which makes it hard to figure out what happened afterwards).
2012-01-25 15:41:08 -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
e349b4b14b
Allow appending with the dbSNP ID even if a (different) ID is already present for the variant rod.
2012-01-25 11:35:54 -05:00
ea3d4d60f2
This annotation requires rods and should be annotated as such
2012-01-25 11:35:13 -05:00
7a26fcb86f
Setting the max alternate alleles for the exact model in the HaplotypeCaller's copy of the UG engine.
2012-01-25 09:51:13 -05:00
bbefe4a272
Added option to be able to write out the active regions to an interval list file
2012-01-25 09:47:06 -05:00
9818c69df6
Can now specify active regions to process at the command line, mainly for debugging purposes
2012-01-25 09:32:52 -05:00
22f0caccac
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-24 16:22:39 -05:00
Mark DePristo
Menachem Fromer
Ryan Poplin
Mauricio Carneiro
Eric Banks
Guillermo del Angel