7ffedf211c
Contig comparator -- sorting contigs like Picard
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This is very useful if you want to output your text files or manipulate data in the usual chromosome ordering :
1
2
3
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21
22
X
Y
GL???
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Just use this comparator in any SortedSet class constructor and your data will be sorted like in the BAM file.
2011-07-24 02:33:19 -04:00
8b8f121cfb
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-21 23:01:11 -04:00
59eb1f4663
Memory limits changed from Int to Double.
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Updated LSF calls to read memory units from config along with tweaks to select hosts.
Moved some common code from GridEngine and LSF to super classes.
2011-07-21 22:57:18 -04:00
87f991aee7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-21 13:35:24 -04:00
2f5d10d16b
Fix bug wherein aligner could be closed prior to its being used to lowercase sequences.
2011-07-21 13:21:48 -04:00
7054c5342f
When using the BWA bindings, you have to explicitly call close() to get the
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bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
2011-07-21 12:13:29 -04:00
84c66d4b92
Bug fixes
2011-07-21 11:52:51 -04:00
c4684f4659
A true oneoff: walker that reads in vcf with multiallelic PL's in wrong ordering and flips them around to output in correct order
2011-07-21 11:20:46 -04:00
15610ce0c3
Per Matt's request, disabling BWA-based integration tests so he can assess bamboo memory usage.
2011-07-21 11:04:22 -04:00
664246937c
Try to resolve merge conflict
2011-07-21 10:19:26 -04:00
32730b1832
Fixed md5 due to new PL ordering
2011-07-20 22:17:15 -04:00
4b0b7f4b32
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 14:49:25 -04:00
f14f20d718
Fix bug involving reuse of the sample variable.
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Cleaned up some otherwise unused comments and code.
2011-07-20 14:48:33 -04:00
0a1d2df8cb
Merged bug fix from Stable into Unstable
2011-07-20 13:19:35 -04:00
f15023b7d2
Bad bug fix: output GLs in multiallelic records were in incorred order (misread spec)
2011-07-20 12:10:48 -04:00
c09f92ccee
Fixing the illegal character accidently entered
2011-07-20 11:39:04 -04:00
4e00666632
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 11:38:16 -04:00
ea90af199c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 11:17:36 -04:00
d3a8363491
Changed MRAV to ADAV
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Updated ReducedBAMEvaluation to allow multiple parameters to be tested
Fixed previous error
2011-07-20 10:49:50 -04:00
b9c9e0e952
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-20 10:45:16 -04:00
7140280bf6
Further bug fixes/cleanups for PrintReadsWalker
2011-07-20 10:44:37 -04:00
a2d90a3590
Bug fix: reverted logic so that default behavior skips over sample lookup
2011-07-20 10:23:10 -04:00
e8409c80fa
Further protection vs null pointers in PrintReadsWalker
2011-07-19 21:59:24 -04:00
5d706c9e92
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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Removing PSP and CSM
Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
2011-07-19 20:25:33 -04:00
fb2d475c22
Bug fix to prevent null pointer
2011-07-19 20:13:56 -04:00
92c7cfa1c8
BWA bindings and tests moved to public (was required for ValidationAmplicons)
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Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.
2011-07-19 20:11:31 -04:00
baae381acb
Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
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This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
2011-07-19 18:38:53 -04:00
eb63b48414
Revert "Resolving conflict"
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This reverts commit 87f0d4a8b0627b3be86acdfef5a9f2fc6ea923ee.
2011-07-19 18:36:53 -04:00
a3cecf0668
Resolving conflict
2011-07-19 17:20:27 -04:00
3d72b98a35
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
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Conflicts:
private/java/test/org/broadinstitute/sting/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java
2011-07-19 17:16:20 -04:00
d92d00a85d
Changed MRAV to ADAV to reflect real implementation (Max reads to Average Depth at Variant Sites).
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Optimized Mapping Quality calculation.
Correctly filtered reads below minimum Mapping Quality threshold
2011-07-19 16:59:06 -04:00
8a7e698883
better debug output for plotting.
2011-07-19 15:28:54 -04:00
07e716d23a
PickSequenomProbes2 expanded functionality: lowercasing based on sequence uniqueness, preserving reference base prior to indel (not a part of the VC as I thought it was), masking deletion bases with 'N's, flanking insertion with 'N's, output is a fasta formatted file. Renamed to ValidationAmplicons since this is really not for picking sequenom probes, but for generating amplicon sequence from which other applications (like sequenom) can choose PCR primers. Moved from private to public.
2011-07-19 15:21:47 -04:00
6181d1e4cb
Fixed integration test for VariantsToTable: now the * in REF column is not output
2011-07-19 14:42:11 -04:00
e6d306458c
Merge bug fixes
2011-07-19 14:36:20 -04:00
989dd17f95
a) Add ability in PrintReads to specify a sample file to easily subset samples, useful for IGV visualization, b) VariantsToTable is more R-friendly with Indels when printing ref/alt columns, c) Changes to SelectVariants ability to speficy a mask to randomly sample from a given AF distribution
2011-07-19 14:29:07 -04:00
005adf377f
Derive MEDIAN_INSERT_SIZE plot from base plot with additional faceting.
2011-07-19 10:48:45 -04:00
9a1394d7e7
Clean up MEDIAN_INSERT_SIZE plot for consistency with other plots.
2011-07-19 10:34:50 -04:00
5d3112c665
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-19 09:32:01 -04:00
0cec2c6759
When sorting samples by date, only use filtered samples to avoid discontinuities
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in the plot. Add brief documentation for running the R script.
2011-07-19 09:28:51 -04:00
9ad5c7dfa4
Resolving simple conflicts in the data processing pipeline.
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Conflicts:
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
2011-07-19 08:05:11 -04:00
7688bda1a6
better progress report for the DPP
2011-07-18 23:39:47 -04:00
2b465ab43b
* added optional 'no validation' for the Data Processing pipeline.
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* some simplifications on the picard classes
2011-07-18 23:30:31 -04:00
4cf7a2af23
Removed broad specific default paths so people from outside the broad can use it.
2011-07-18 23:25:21 -04:00
9b446020f9
Using picard implementations for accessing aggregation directories.
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Added more utilities to PicardPrivate.
Revved picard.
2011-07-18 21:49:03 -04:00
0ef37979cc
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 21:30:51 -04:00
d5d107856c
Subselect based on bait set.
2011-07-18 18:42:21 -04:00
1837da37f6
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-18 17:59:26 -04:00
916c0c9489
some quick & dirty debug info for the replication validation walker.
2011-07-18 17:57:12 -04:00
044f5faa4d
Support for numeric columns.
2011-07-18 17:44:49 -04:00
Mauricio Carneiro
Khalid Shakir
Guillermo del Angel
Christopher Hartl
Matt Hanna
Roger Zurawicki
David Roazen