b0560f9440
Rev. tribble to fix BED codec bug in tribble 51
2012-01-17 16:40:26 -05:00
f2b0575dee
Detect unreasonably large allele strings (>2^16) and throw an error
...
-- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places.
-- Tribble was updated so we actually could read the line properly (rev. to 51 here).
-- Still the parsing algorithms in the GATK aren't happy with such a long allele. Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.
2012-01-17 16:40:26 -05:00
e923a2e512
Revving Picard to incorporate final version of ReadWalker performance improvements.
2012-01-10 12:12:33 -05:00
ea6e718cb8
SnpEff 2.0.5 support. Re-enabled SnpEff in the HybridSelectionPipeline.
...
For now, we recommend only running with the GRCh37.64 database.
2012-01-03 15:18:36 -05:00
e6e80e8d3f
Update Picard to fix a bug Mauricio found in Picard where Picard unnecessarily depends on Snappy during some usages of SortingCollection.
2011-12-29 14:35:02 -05:00
b4b7ae1bd9
Revved Picard to incorporate tfennell's AsyncSAMFileWriter.
...
Removed DbSnpFileGenerator and related files as they were removed from PPP r2063 by ktibbett.
2011-12-06 10:37:42 -05:00
c9eae32f6e
Revving Tribble to actually close file handles when close() is called.
2011-11-30 22:42:21 -05:00
d7d8b8e380
Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.
2011-11-28 14:18:28 -05:00
68b2a0968c
Updating the HybridSelectionPipeline for SnpEff 2.0.4 RC3
...
This will have to be done again when the 2.0.4 release becomes official,
but it's necessary to do now in order to re-enable the pipeline tests.
2011-11-17 14:46:12 -05:00
d64f8a89a9
Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly.
2011-11-09 15:24:29 -05:00
6297561326
Adding the new jar
2011-11-07 15:08:19 -05:00
aa0c8c3600
Revving Tribble jar to v40. Our last jar was busted.
2011-11-07 11:30:08 -05:00
9afe6fc7ac
Picard upgrade to 1.55.
2011-10-24 17:02:27 -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.
...
Updates to HybridSelectionPipeline:
- Added annotations back via snpEff
- Minor updates to VQSR paths and lowered memory
2011-09-27 14:33:57 -04:00
34f435565c
Accidentally committed unclean tribble jar to repo
2011-09-21 10:16:17 -04:00
827c942c80
Rev tribble
2011-09-20 14:01:14 -04:00
da9c8ab386
Revving the Tribble jar where the DbsnpCodec class was renamed to OldDbsnpCodec. Updating GATK code accordingly.
2011-09-06 20:39:42 -04:00
0b794b5491
Reving Tribble to 23
2011-09-01 10:43:03 -04:00
d604019362
Finished my broken tribble code. Updated to rev 22
2011-08-30 16:56:48 -04:00
bdf04b8057
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-30 11:08:23 -04:00
173ca1e215
Reverting tribble temporarily while I fix my subtle problems
2011-08-30 11:08:13 -04:00
2125ba1f23
Merged bug fix from Stable into Unstable
...
Conflicts:
private/java/src/org/broadinstitute/sting/pipeline/ReferenceData.java
2011-08-29 19:36:43 -04:00
20ac24464d
Rev'ved picard to read new analysis_files.txt with a blank line after header and no reference sequence.
...
Updated error messages and unit tests.
2011-08-29 19:33:04 -04:00
427c643ce7
The missing tribble jar
2011-08-29 18:46:40 -04:00
5defaf5fac
Continuing to improve Tribble
...
-- ProfileRodSystem now has a just load index mode, allowing us to optimize the profiler
-- assessFarmNodes R script for making nice plots of performance of jobs on the farm
-- Rev. tribble to use new, optimized index loading (performance win when loading many many indices)
2011-08-29 17:02:57 -04:00
bd5cdb8a43
The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml
2011-08-11 16:38:29 -04:00
baae381acb
Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable"
...
This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
2011-07-19 18:38:53 -04:00
9b446020f9
Using picard implementations for accessing aggregation directories.
...
Added more utilities to PicardPrivate.
Revved picard.
2011-07-18 21:49:03 -04:00
00b650a35d
Get rid of accidental commit of emacs backup '~' file.
2011-07-17 20:52:46 -04:00
567ed66085
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-17 20:44:43 -04:00
0a0363aef2
Revving Picard to get a parser that works with the latest metrics file formats
...
we're starting to see.
2011-07-17 20:43:35 -04:00
35ec82a467
Oops, need this
2011-07-17 13:08:08 -04:00
4db2b13e9e
Rev tribble.
...
Just added more documentation for diffEngine and pointer to new wiki:
http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
2011-07-17 13:05:04 -04:00
a5bfcb1ed9
V15 is broken. Going up to v16 in a second.
2011-07-17 10:25:34 -04:00
2b55d5b7c0
Test tribble library where equals() ignores time stamps.
2011-07-16 16:45:55 -04:00
07b875c779
Renaming the updated tribble jar file to match the svn revision number.
2011-07-16 09:57:46 -04:00
5e7bc862a3
Rev tribble to include new equal() method that prints out details of why two indices are not the same.
2011-07-16 08:51:21 -04:00
68e19edf59
Merged bug fix from Stable into Unstable, and resolved merge conflicts.
...
Conflicts:
build.xml
settings/ivysettings.xml
2011-07-08 15:50:31 -04:00
a3c9d9c3ff
Fixing Contracts for Java, and enabling contracts by default for unit/integration tests.
...
The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.
To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.
Also did some minor unrelated cleanup in build.xml
2011-07-08 15:34:39 -04:00
7b699f8b17
Switched GridEngine from looking from environment variable to using embedded jar.
2011-07-05 21:59:00 -04:00
643458d7db
Updated the tribble jar -- this should fix most of the integration test
...
failures we've been seeing.
Note that with tribble's new svn repository the revision numbers have reset,
hence "revision 3"
2011-06-29 01:11:03 -04:00
171e20a111
Updated the tribble jar to revision 351
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6068 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:57 +00:00
ab1de3bfda
Updated the tribble jar to revision 350
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6065 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:46 +00:00
95614ce3d6
Updated the tribble jar to revision 345
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6033 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:53:25 +00:00
32a991c4d3
Updated the tribble jar to revision 343
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6031 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:53:17 +00:00
14d7ee073b
Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script
...
to incorporate PF_INDEL_RATE.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5998 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:43:43 +00:00
cde2b409a7
Oops. Failed to add DbSnpMatchMetrics to Picard private jar.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5994 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 15:14:19 +00:00
1b1aefc385
Move fingerprinting metrics reader into our Picard private extract.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5990 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 00:13:10 +00:00
480598842c
Updated the tribble jar
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5982 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-13 18:00:09 +00:00
Mark DePristo
Matt Hanna
David Roazen
Khalid Shakir
Eric Banks
droazen
hanna