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
fc86cd6fd8
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/carneiro/gatk/RR into rr
2011-09-29 00:12:15 -04:00
4fd5630f6a
Added ReadClipper Unit Test
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* Includes tests that include HardClip to Read and Reference Coords.
* Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing
2011-09-28 23:13:50 -04:00
f49a12de6b
Updating latest changes from the repository to reduce reads repo
2011-09-28 22:31:57 -04:00
9272ed03b5
Merged bug fix from Stable into Unstable
2011-09-28 21:26:43 -04:00
0acaf2df65
Fix an embarrassing issue where a specific configuration of minimal coverage
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over small intervals could cause reads to be dropped from the pileup. Nothing
to see here...
2011-09-28 21:23:01 -04:00
07b0a75d96
Added SlidingRead Unit Test
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Includes test clipStart and trimToVariableRegion
2011-09-28 21:22:57 -04:00
c5f1a4325f
Updated preQC:
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- full 8.5x11
- concating multiple initiatives / bait_sets
- Using NA instead of python None when WR dates are unavailable
- In new aggregations where the sample may have per library metrics, only using the sample level metrics, i.e. library is null
Updated postQC:
- Renamed some variables to assist with traceback()
- Fixed crashes on batches with two alleles or two samples such as Seminara_MC_1_09222011 or Engle_MC_2_09222011
- Added dependency tracking to PostCallingQC.scala so that the R script does try to run before the evals are complete
Other minor cleanup.
Tried to use R 2.13 compactPDF but a few issues to work out with fingerprint boxplots in preQC and geom_text font size in postQC.
2011-09-28 20:23:30 -04:00
edf852d47d
Adding lists to ReduceReads script
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script can handle single file or list of files separately now. Always scatter/gathering.
2011-09-28 18:40:30 -04:00
64e7b3000c
Fix read spans deletion through the entire interval
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if the read has a deletion that spans the entire length of the interval, it should not be added to mapped reads.
2011-09-28 18:40:30 -04:00
a93ece07e3
ScatterGatherable reduce reads script
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Get your reduce read in a matter of seconds...
2011-09-28 18:40:30 -04:00
c8d3a720f9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-28 18:17:34 -04:00
7e3cb45093
Further performance optim in banded hmm, about 60% speed improvement over current implementation now
2011-09-28 16:27:28 -04:00
1b1ca80df2
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-28 16:17:39 -04:00
3b73dc89fe
Making several esoteric arguments in the BQSR @Hidden. Adding basic support for Complete Genomics machine cycle.
2011-09-28 16:17:31 -04:00
ff2f4df043
Fixed hardclipping inside indel (right tail)
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when hard clipping the right tail of a read falls inside a deletion, clipping should fall back to the last base before the deletion to follow the ReadClipper's contract.
2011-09-28 16:07:34 -04:00
3c7b7f74ef
Optimized interval iteration
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Using a TreedSet to manipulate getToolkit.getIntervals() and being smart about which intervals to test makes interval clipping O(1) instead of O(n).
2011-09-28 16:07:34 -04:00
5c9b659c02
clipping both ends of the reads was modifying the original read
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This goes against the ReadClipper contract, and was affecting the second part of the read that spans over multiple intervals. Fixed.
2011-09-28 16:07:34 -04:00
fe23e4d10c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-28 15:53:11 -04:00
e2b9030e93
First mostly fully functional implementation of banded pair HMM likelihood computation for indel caller. More experimentation to follow but it right now works in small data sets and at least it doesn't break existing things. Disabled by default at this point
2011-09-28 15:51:48 -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
ceffefa6a6
Intermediate version with banded pair HMM
2011-09-27 10:18:58 -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
Mark DePristo
Mauricio Carneiro
Roger Zurawicki
Matt Hanna
Khalid Shakir
Guillermo del Angel
Ryan Poplin
Eric Banks