53e6d66601
analyzeRunReports pushes full stack trace to DB for reporting
...
-- Minor parsing changes to handle this.
2012-02-03 12:32:33 -05:00
79da5ca2ae
Parses major and minor GATK versions now. Added unit tests
2012-02-03 12:32:31 -05:00
3abfbcbcf2
Generalized the TDT for multi-allelic events
2012-02-03 12:23:21 -05:00
f596377e73
Oops. Forgot that some samples are new and the data directory doesn't already exist. Now try to create it if it's not already present.
2012-02-02 12:39:49 -05:00
1f50f6970b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-02 10:17:13 -05:00
4ed06801a7
Updating HaplotypeCaller's HMM calc to use GOP as a function of the read instead of a function of the haplotype in preparation for IQSR
2012-02-02 10:17:04 -05:00
d1a1888d2f
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-02 09:58:22 -05:00
48220700eb
Adding lftp to the supported download protocols for the 1000G sync. Initial results look very good! Bringing down chrom11 and chrom20 files now.
2012-02-02 09:58:03 -05:00
8adfc79123
Merged bug fix from Stable into Unstable
2012-02-01 16:07:41 -05:00
30b937d2af
Fix bug discovered in FGTP branch in which BlockInputStream returns -1 in cases where some data could be read,
...
but not all the data requested by the caller.
2012-02-01 16:06:22 -05:00
2109122cdd
merging branches
2012-02-01 14:37:24 -05:00
bc6abc94e9
Bug fix for check of isMateUnmapped. Requires check of mate is mapped.
2012-02-01 14:32:19 -05:00
a46a29501b
Marking unused code in HC for removal.
2012-02-01 13:22:17 -05:00
45da892ecc
Better exceptions to catch malformed reads
...
* throw exceptions in LocusIteratorByState when hitting reads starting or ending with deletions
2012-02-01 11:56:19 -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
e8528bc526
updating HaplotypeCaller integration tests
2012-02-01 09:43:19 -05:00
dc23265640
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-01 09:22:43 -05:00
579627568e
Limit to 3 ALT alleles
2012-01-31 23:39:39 -05:00
08c7c07f25
Added the option of not compressing read names to ReduceReads
...
* When scatter/gathering, name compression cannot guarantee uniqueness. If uniqueness is important, it is recommended to turn compression off for scatter/gathering ReduceReads.
2012-01-31 17:14:57 -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
a7f5d26326
No more synthetic reads starting/ending with deletions
...
bug reported by Kristian Cibulskis that we were generating filtered data synthetic reads with leading deletions. Added integration test.
2012-01-31 11:41:36 -05:00
2f2f039c37
Better flow for byNegTrainingFraction
2012-01-31 10:49:46 -05:00
d8a4d78854
Bugfix for exceptions with unknown source whose error was not being shown in tableau
2012-01-31 10:49:06 -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
e7ace8efc4
Fix NullPointerException caused in cases with too many ALT alleles
2012-01-30 21:00:16 -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
...
discordance now reports discordance between genotypes as well (just like concordance)
2012-01-30 09:50:45 -05:00
f1e07f169e
Only apply filters if there are filters to apply
2012-01-30 02:22:13 -05:00
d1aa5204d7
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-29 23:39:34 -05:00
3186f0f1b0
Try more memory and fewer ALT alleles so that we don't run out of memory
2012-01-29 23:38:32 -05:00
3164c8dee5
S3 upload now directly creates the XML report in memory and puts that in S3
...
-- 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
...
* 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
...
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"
...
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
Mark DePristo
Eric Banks
Ryan Poplin
Matt Hanna
Mauricio Carneiro
Christopher Hartl
Menachem Fromer