5343f8ba67
Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
2012-02-05 13:09:03 -05:00
2cd33b2f1f
Better display of LSF usage for gsafolk
2012-02-04 08:22:55 -05:00
f94d547e97
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 17:14:20 -05:00
894d3340be
Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.
2012-02-03 17:13:52 -05:00
4a57add6d0
First implementation of DiagnoseTargets
...
* calculates and interprets the coverage of a given interval track
* allows to expand intervals by specified number of bases
* classifies targets as CALLABLE, LOW_COVERAGE, EXCESSIVE_COVERAGE and POOR_QUALITY.
* outputs text file for now (testing purposes only), soon to be VCF.
* filters are overly aggressive for now.
2012-02-03 17:12:43 -05:00
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
...
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
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
...
-- 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
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,
...
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
...
* 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
Ryan Poplin
Mark DePristo
Mauricio Carneiro
Christopher Hartl
Eric Banks
Matt Hanna
Menachem Fromer