e76f381628
Moved sample package from DataSources to gatk, and renamed it samples
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-- All associated changes to the codebase are just header updates
2011-09-29 09:57:15 -04:00
e197dcd1f3
Pre-cleanup commit of Sample and SampleDataSource
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-- SampleDataSource has all reader functionality disabled
2011-09-29 09:44:18 -04:00
4d31673cc5
No longer supporting YAML file allows us to delete 75% of the sample's codebase
2011-09-29 09:43:31 -04:00
1b45f21774
Removing this command-line tool. Purposely not doing this in stable so that users who may still use it have time to find other options. But the docs are no longer on the wiki.
2011-09-28 13:18:32 -04:00
1f0e354fae
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-28 13:13:21 -04:00
bb619a9a3c
Fixing docs
2011-09-28 13:13:03 -04:00
5812004e06
Merge branch 'stable'
2011-09-28 11:36:40 -04:00
a88b7c1203
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-28 11:36:33 -04:00
a5006831d7
Shows "" not empty space when default string value is ""
2011-09-28 11:35:52 -04:00
1e32281a15
Fix to not show -null when missing short name argument
2011-09-28 11:31:20 -04:00
89544c209c
Fixing contracts
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changed return type to Pair, changing contracts accordingly.
2011-09-28 11:19:17 -04:00
2e2463633f
Queue script to find missing calls between full and reduced bams
2011-09-28 11:17:25 -04:00
eacbee3fe5
Merged bug fix from Stable into Unstable
2011-09-27 20:35:18 -04:00
43b0c98298
Fix docs
2011-09-27 20:34:46 -04:00
232a6df11c
Add longhand form to the error message.
2011-09-27 20:29:31 -04:00
1d6fcb6eb1
Revert "Add longhand form to the error message to prevent users from posting borderline dumb posts to GS."
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This reverts commit 75b2600527cfce05ae683cb394290ff2a80e8552.
2011-09-27 20:27:00 -04:00
269b9826b6
Add longhand form to the error message to prevent users from posting borderline dumb posts to GS.
2011-09-27 20:26:36 -04:00
3b6e43b7c4
Use reads that span multiple intervals
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* RR will now compress reads that span across multiple intervals correctly and output them in the correct order.
* Fixed bug in getReadCoordinateForReferenceCoordinate where if the requested reference coordinate fell inside a deletion in the read the read would be clipped up to one element past the deletion.
2011-09-27 18:39:06 -04:00
84bd355690
Merged bug fix from Stable into Unstable
2011-09-27 14:34:39 -04:00
b090751f62
Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.
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Updates to HybridSelectionPipeline:
- Added annotations back via snpEff
- Minor updates to VQSR paths and lowered memory
2011-09-27 14:33:57 -04:00
db785eb50d
Fix a bug where no fingerprint LODs across an entire project would cause the
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R script to blow up.
Also, correct the sample names displayed at the bottom of the fingerprint plot;
previously, it displayed the order of the sample in a sequence sorted by
last sequencing date.
2011-09-27 12:39:25 -04:00
e5ce5e265a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-27 11:07:01 -04:00
26e71f6688
The Omni files have multiple records (with the same ALT) at a particular location, with one PASSing and the other(s) filtered. Chris, this is why using this file as both eval and comp leads to ref/no-call cells in the GenotypeConcordance table. However, this led to non-determinism in VE because the VCs were placed in a HashSet; we use a LinkedHashMap instead to bring back determinism.
2011-09-27 11:03:17 -04:00
e99ff3caae
Removed lots of old, and not to be used, HMM options
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-- resulted in massive code cleanup
-- GdA will integrate his new banded algorithm here
-- Removed: DO_CONTEXT_DEPENDENT_PENALTIES, GET_GAP_PENALTIES_FROM_DATA, INDEL_RECAL_FILE, dovit, GSA_PRODUCTION_ONLY
2011-09-27 10:08:40 -04:00
17dc0e44bc
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-27 07:10:58 -04:00
77ba59e30a
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-27 00:51:45 -04:00
648b959361
Minor change to log an info message when a signal such as Ctrl-C is caught.
2011-09-27 00:50:19 -04:00
6d8b3b882f
Merged bug fix from Stable into Unstable
2011-09-26 15:16:54 -04:00
6478681c0c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-09-26 15:12:52 -04:00
82bb3acba0
Merged bug fix from Stable into Unstable
2011-09-26 14:59:23 -04:00
059cdcb1be
Changing packaging system path for GATK-only Tribble codecs.
2011-09-26 14:58:19 -04:00
fa0efbc4ca
Refactoring of PairHMM to support reduced reads
2011-09-26 13:28:56 -04:00
a6b65d6347
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-26 13:26:21 -04:00
4f09453470
Refactored reduced read utilities
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-- UnitTests for key functions on reduced reads
-- PileupElement calls static functions in ReadUtils
-- Simple routine that takes a reduced read and fills in its quals with its reduced qual
2011-09-26 12:58:31 -04:00
234b74dd05
Merged bug fix from Stable into Unstable
2011-09-26 11:47:23 -05:00
317b95fa57
Fixing some annotator docs
2011-09-26 11:46:45 -05:00
763fcfc96b
Adding support to splitting one read into multiple reads
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This framework will be necessary for adding features like a read that spans multiple intervals.
2011-09-26 09:24:40 -04:00
b76dbc72f0
Fixed interval navigation bug.
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If a read was hard clipped away from the current interval, all subsequent reads within that interval (not hardclipped) would be filtered out. Fixed.
2011-09-26 08:13:44 -04:00
9afccd11b1
Minor refactoring: add ability to MathUtils.normalizeFromLog10 to not go to linear domain but just substract max value from log values and return. Use this function in snp and indel GL computation.
2011-09-25 21:18:56 -04:00
8c4eb5827f
cleaning up parameter/variable names
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making things more uniform.
2011-09-24 23:41:21 -04:00
3eedb40c3e
Cleaning up old code from ReduceReads
2011-09-24 23:41:20 -04:00
3eef800889
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-24 21:20:11 -04:00
4707ab4a7d
Added unit tests to test genotype merges with PL's
2011-09-24 21:17:15 -04:00
203517fbb7
a) Cleanups/bug fixes to previous commit to CombineVariants.
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b) Change md5 to reflect records that are now merged correctly.
c) Change unit merge alleles test to reflect the fact that a null non-variant vc object is not valid and not supported because there's no way to codify such object in a vcf. The code correctly converts this to a non-variant single-base event with whatever the reference is at that location.
2011-09-24 19:08:00 -04:00
466ffa3665
Forgot to hide my (shameless) debug techinque
2011-09-24 14:39:42 -04:00
c31f4cb2f6
Cleaning leading insertions
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With the current implementation, a read cannot start with a deletion or an insertion. Maybe this will change in the future, but for now, chop the leading insertion off.
2011-09-24 14:33:32 -04:00
cd058dd10f
a) Fixed md5 for legit change in UG output that now also no-calls genotypes w/0,0,0 in PL's in SNP case.
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b) First reimplementation of new vc merger of different types. Previous version did it in two steps, first merging all vc's per type and then trying to see if resulting vc's would be merged if alleles of one type were a subset of another, but this won't work when uniquifying genotypes since sample names would be messed up and GT sample names wouldn't match VC sample names. Now, it's actually simpler: when splitting vc's by type before merging, we check for alleles of one vc being a subset of alleles of vc of another type and if so we put them together in same list.
2011-09-24 13:40:11 -04:00
bb11951255
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-24 09:26:45 -04:00
8d9e136bba
Merge branch 'stable'
2011-09-24 09:26:28 -04:00
6804ab6d2f
Bug fix for NPE in very short GATK runs
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-- Was already in unstable, but not stable...
2011-09-24 09:25:29 -04:00
Mark DePristo
Eric Banks
Mauricio Carneiro
Khalid Shakir
Matt Hanna
Guillermo del Angel