7b92cd5008
Adding lucene dependency for file locking -- may be removed in the near future
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5065 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 18:59:42 +00:00
61fe409211
Basic walker to count the number of (phased) hets in each exome target
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5064 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 17:53:14 +00:00
c50f39a147
V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5063 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 16:45:07 +00:00
fd864e8e3a
Minimal necessary (but most likely not sufficient) changes to run VQSR on indel data: don't fill Ti/Tv fields if non-SNP, request VC only st start of position, check if isSNP() before doing snp-specific operations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5062 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 02:36:36 +00:00
a51061fd96
Improved distributed processing analytics. Still not 100% ready for prime-time. More improvements incoming. Iterator claim now supports requests to obtain in a single atomic claim (one lock) multiple sequential shards, which radically reduces overhead. However, deadlocking is still possible...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5061 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 16:17:25 +00:00
2d4bcb60a1
Don't print out alt alleles for ref calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5060 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 06:33:31 +00:00
2ba35dc7ba
Bad chain files are user errors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5059 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 06:04:36 +00:00
2bbcc9275a
Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5058 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 05:04:17 +00:00
bb6999b032
Better documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5057 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 03:36:09 +00:00
1dcdebbc9e
Updating the file path for proper inclusion of the background in the tearsheet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5056 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-22 19:15:33 +00:00
c52d2d5f79
Bug fix for SimpleTimer that didn't always convert elapsed times from milliseconds to seconds
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5055 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-22 18:50:59 +00:00
ff61aeb762
continuing to push to get right answers for long-running jobs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5054 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-22 15:02:02 +00:00
a50d7f74fa
Change to support plotting of indel quality as a function of covariates - for now, just call different R calling script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5053 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-22 14:09:23 +00:00
fa0c476b82
Script for calling indels in all phase 1 samples - VQSR part still needs work but raw calling is done
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5052 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-22 14:07:10 +00:00
9b1b8d46aa
Performance tracking of GenomeLocProcessingTrackers, as well as a marker for where to put tracker in HierarchicalMicroScheduler
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5051 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 22:24:42 +00:00
95d6ddc38c
lastProgressPrintTime should only be updated when a progress log is printed not when a performance log is printed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5050 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 22:23:14 +00:00
8ece2b9230
Distributed GATK analysis scripts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5049 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 22:09:07 +00:00
a0731eaa81
updated NA12878 Trio gold standard data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5048 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 18:48:31 +00:00
94b64ec54a
Moving scala script into analysis directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5047 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 18:42:18 +00:00
63e8103c4e
A new top-level directory to hold analysis scripts associated with specific analyses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5046 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 18:40:02 +00:00
b45566760e
intermediate checkin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5045 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 18:39:25 +00:00
6fbd18c759
Cleaning up obsolete code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5044 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 16:27:35 +00:00
8d46cf3604
Testing a configuration change for build system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5043 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 14:44:41 +00:00
78a43faebe
Adding options to warn instead of erroring out (so that you can see all errors in one shot) and to skip filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5042 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 05:24:28 +00:00
02b5d4357f
Deprecated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5041 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 05:05:07 +00:00
c3dbbe7f91
Bug fix: don't assume users won't use arbitrary rods on the commandline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5040 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 04:59:28 +00:00
b6497c404f
Moving Phase1Calling qscript over to using the cleaned, pre-BAQed bams
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5039 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 02:41:20 +00:00
aea121a9d5
<key>=<value> tagging support for command-line arguments. Unfortunately, still
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very hard to validate and still very hard to use (requires core hacking to
support additional tags).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5038 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 00:22:42 +00:00
fc73569d62
Added NA12878 Trio dataset to the pipeline.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5037 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 23:15:33 +00:00
8855f080c2
For the fullCallingPipeline.q:
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- Reading the refseq table from the YAML if not specified on the command line.
- Removed obsolete -bigMemQueue now that CombineVariants runs in 4g.
- Added a -mountDir /broad/software option to work around adpr automount issues.
- Merged the LSF preexec used for automount into the shell script used to execute tasks.
- Using the LSF C Library to determine when jobs are complete instead of postexec.
- Updated queue.sh to match the changes above.
- Updated the FCPTest to match the changes above.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 22:34:43 +00:00
8831ec3dce
Some refactoring and cleanup around the area of my sleep-deprived integration
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test typo, which Khalid already fixed for me. Sorry, Khalid!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5035 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 15:03:14 +00:00
3022f4dfa0
Fixed missing space character in testSimpleVCFStreaming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5034 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 14:49:38 +00:00
e4ac1e6171
Removing unused file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5033 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 13:03:55 +00:00
85553cf5cb
V2 cleaner, easily testing, shared memory and distributed GATK job management. Serious unit testing. Very much cleaner processing. Some code cleanup remains in removing now unused classes but the system is ready for general testing. Confirmed that one can run the UG 100 ways parallel without error, but edge cases may remain.
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See documentation at:
http://www.broadinstitute.org/gsa/wiki/index.php/Parallelism_and_the_GATK#Distributed_Parallelism_.28Experimental.29
for examples on how to run this, or the testing Scala script
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5032 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 12:58:13 +00:00
41c8552d0a
Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5031 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 12:54:03 +00:00
cacdac3914
Major refactoring of shards. No longer uses interfaces but is now an actual object hierarchy with most of the important and common functionality pushed up to base classes. Eliminated a lot of duplicated code, and the shards are much more understandable now. Also now require a GenomeLocParser to work with their own GenomeLocs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5030 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 12:36:56 +00:00
4d611e53e7
Passing the ADPR R script to FCPTest.
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Changed the FCP.q to use an InProcessFunction work around the -runDir issue GSA-420.
Tested the FCPTest using the following dotkits and "ant clean pipelinetest -Dpipeline.run=run":
- R-2.11
- Oracle-full-client
- .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5029 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 06:08:45 +00:00
7087c2f422
Very simple integration tests for basic VCF streaming functionality.
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Rather than try to fork the integration test process to get a pipe source
and sink, creates a new named pipe by Runtime.exec()ing the 'mkfifo' shell
command. We'll see whether this proves to be a reliable method for testing
streaming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5028 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 04:38:54 +00:00
acc2f1c9fe
Updated FCPTest to use the new path to fullCallingPipeline.q changed in r5017.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5027 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 21:43:43 +00:00
22582960be
Adding the backdrop to the current version of the tearsheet so it is always available
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5026 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:56:11 +00:00
2824e8224c
removes unused titv argument
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5025 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:49:12 +00:00
50fcebb0c4
Incorporates tearsheet and plot production with database access into standard pipeline. Note that the following dotkit packages must be run before the adpr will be correctly generated:
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R-2.10,
Oracle-full-client,
cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1
This also removes the unused titv argument
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5024 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:48:42 +00:00
2b895ffb7f
Updated the HG19 reference from v0 to v1 after the v0 was zeroed out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5023 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:30:25 +00:00
af60666f5d
An example template for the shell script used to run the full calling pipeline on the broad system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5022 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:28:59 +00:00
dfcd45181a
Some minor tweaks to the tearsheet generator that incorperate the gsalib more universally and create a more accurate output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5021 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 20:27:02 +00:00
c901fb6d70
Now populating the refseq and dbsnp in awk instead of retrieving from firehose.
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Added refseq table to the pipeline object.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5020 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 18:19:10 +00:00
55eb0387ac
Another relevant qscript. I use this one to do thousands of variant recalibration jobs to search for optimal parameters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5019 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 18:17:32 +00:00
82f81a83c2
Mauricio shall not escape my vengeance!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5018 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 15:24:37 +00:00
a463dbcda1
Refactoring the qscript directory; oneoffs, playground, and core
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5017 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 15:23:40 +00:00
24bc843ae8
Dynamically change the log message update rate so that short jobs receive frequent updates while longer running jobs receive fewer updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5016 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-19 15:09:11 +00:00
depristo
fromer
delangel
ebanks
corin
rpoplin
carneiro
kshakir
hanna
chartl