3dd6a1f962
Adding some generic sum and average functions to MathUtils
2012-02-03 17:12:43 -05:00
e1d69e4060
make the size of a GenomeLoc int instead of long
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it will never be bigger than an int and it's actually useful to be an int so we can use it as parameters to array/list/hash size creation.
2012-02-03 17:12:42 -05:00
92e3e5e565
Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable
2012-02-03 15:48:22 -05:00
5af3999a2d
updating HaplotypeCaller integration tests
2012-02-03 14:04:58 -05:00
0e44430e47
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 13:45:11 -05:00
aa3638ecb3
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 13:42:09 -05:00
53e6d66601
analyzeRunReports pushes full stack trace to DB for reporting
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-- 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
601e53d633
Fix when specifying preset active regions with -AR argument
2012-02-02 16:34:26 -05:00
974c2499cc
Bugfixed to script.
2012-02-02 12:55:54 -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
27ea6426a4
Small script to chunk up a VCF into equal-sized chunks
2012-02-02 12:29:03 -05:00
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
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
45bf2562cc
.
2012-02-02 09:11:17 -05:00
f8c5406084
Add the ability to extract samples
2012-02-02 09:06:39 -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,
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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
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
45da892ecc
Better exceptions to catch malformed reads
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* 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
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* 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.
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Thanks to Ryan for pointing this out.
2012-01-31 11:58:21 -05:00
a7f5d26326
No more synthetic reads starting/ending with deletions
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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
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* 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
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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
Mauricio Carneiro
Christopher Hartl
Ryan Poplin
Mark DePristo
Eric Banks
Matt Hanna
Menachem Fromer