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
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
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
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
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
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
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
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
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
f8ba76d87c
Incremental commit for distributed computation. Appears to work but has potential deadlock situation not yet debugged. Do not use yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5010 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-17 21:23:09 +00:00
a88708ebfa
Moving GLF code to archive
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5006 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-15 22:42:42 +00:00
af31d02a2d
Fix concurrency issue that periodically kills VariantEvalIntegrationTest --
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a member field of RMDTrackBuilder was getting rebuilt every time it was
called, creating concurrency issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5001 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 18:52:21 +00:00
af1bce3492
Longer wait time for threading test (5 min now) and an assertion to ensure that all jobs finished. Should probably just remove the longer running test so this becoming a non-issue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4999 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 13:09:31 +00:00
afbea9ce59
SharedMemory and SharedFile implementations of GenomeLocProcessingTracker, along with serious unit tests that both pass. Slightly inefficient implementation but sufficient for further testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4998 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 03:14:24 +00:00
02dc0f97d1
Remove testWalkerUnitTest; it doesn't actually do anything and just adds
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extra cruft to the output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4993 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 19:02:00 +00:00
ce3d226183
Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4984 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:12:30 +00:00
edebbb5aa0
Fixed long-standing bug reported by Mauricio where @Arguments assigned to
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primitive types were properly validated and throw the proper
MissingArgumentValue UserException. Before this fix, the error reported
was the infamous DePristo BSOD (Could not create module String because
an exception of type NullPointerException occurred caused by exception null).
Thanks Mauricio!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4980 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 22:18:24 +00:00
6d855041ec
Oops...forgot to commit the changes that allow primitive VCF streaming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4979 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 21:54:51 +00:00
8fe5641b2e
can explicitly set the now required ReferenceDataSource in unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4977 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 18:25:12 +00:00
7916ab0ed5
remove the index each run
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4976 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 17:38:22 +00:00
468ef382b7
vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4975 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 17:32:27 +00:00
5e9a8f9cb3
Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.
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Adding the first version of the techdev pipeline (tdPipeline)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 22:25:08 +00:00
cba436fa2f
small fix for the table codec; if you see a header line, you know you've finished parsing the header. Also also some changes to return the ref ordered data pool test to using MappedStreamSegment instead of EntireStream
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4942 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 21:20:26 +00:00
0982d35f5b
Bug fixes in streaming in Tribble data via /dev/stdin.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4935 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 02:43:04 +00:00
23dbc5ccf3
HaplotypeScore is revamped. It now uses reads' Cigar strings when building the haplotype blocks to skip over soft-clipped bases and factor in insertions and deletions. The statistic now uses only the reads from the filtered context to build the haplotypes but it scores all reads against the two best haplotypes. The score is now computed individually for each sample's reads and then averaged together. Bug fixes throughout. The math for the base quality and mapping quality rank sum tests is fixed. The annotations remain as ExperimentalAnnotations pending more investigation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4934 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 00:28:05 +00:00
8d2c14b29c
Update Picard / sam-jdk at Tim's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 02:17:25 +00:00
3fc9862964
Unit test fixed - Tribble codecs aren't designed to be stateless, but I was
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using one as though it was. Fixed, and debug code reverted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4917 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 17:47:52 +00:00
b9cb57f4b9
A unit test is failing on bamboo in a way I can't reproduce (or even explain).
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Checking in some debugging info.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4916 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 16:35:04 +00:00
cba18116e4
A significant refactoring of the ROD system, done largely to simplify the process of
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streaming/piping VCFs into the GATK. Notable changes:
- Public interface to RMDTrackBuilder is greatly simplified; users can use it only to build
RMDTracks and lookup codecs.
- RODDataSource and RMDTrack are no longer functionally at the same level; RODDataSources now
manage RMDTracks on behalf of the GATK, and the only direct consumers of the RMDTrack class
are the walkers that feel the need to access the ROD system directly. (We need to stamp out
this access pattern.
A few minor warts were introduced as part of this process, labeled with TODOs. These'll be
fixed as part of the VCF streaming project.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4915 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-31 04:52:22 +00:00
848977678d
No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4913 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 22:06:19 +00:00
8a0c07b865
Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4908 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-27 07:37:46 +00:00
e313eeede8
Push command-line expansions, such as BAM list unpacking and -B tag parsing, out
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into the CommandLine* classes. This makes it easier for external functionality
(such as the VCF streamer) to use GenomeAnalysisEngine directly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4897 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 19:00:17 +00:00
a3729bd59c
Now I call BeforeMethod correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4872 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 22:45:45 +00:00
b7e4a015c0
static thread cache reset in UnitTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4870 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 21:53:10 +00:00
3bbc6a0540
Slightly more thread safe CachingIndexedFastaSequenceFile.java. Likely passes parallel testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4869 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 21:05:17 +00:00
5dd0e8388b
Fixed a bug in UnitTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4867 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 19:44:35 +00:00
4a54f3f230
ThreadLocal version of CachingIndexedFastaSequenceFile. More efficient support for shared memory BAQ calculations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4865 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-17 15:44:48 +00:00
acfe83920b
'-L unmapped': adding integration tests for explicitly including (-L unmapped)
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unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting
the suite of unit tests already put in place.
'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 23:11:46 +00:00
5c0b66cb7c
3 big changes that all kill the integration tests: 1. Don't cap the PLs by 255 anymore. 2. Move over to the 3state model as the only available base model for UG (no more base transition tables). 3. New QD implementation when GLs/PLs are available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4846 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 16:24:28 +00:00
5a27d231fa
Rename it so that nobody else falls into the trap laid out (the test is VariantToTable, the walker is Variant[s]ToTable)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4844 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:43:00 +00:00
5e27e9162f
Huh? I thought we parsed out comma-separated command line arguments into list automatically...just change the syntax of the integration test, no need to update the md5
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4843 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:40:27 +00:00
01323447c6
Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
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Fixed integration tests to wait on their own for the job to run instead of using SUB2_BSUB_BLOCK.
Updated VariantRecalibrationIntegrationTests MD5s which were knocked out of sync whele SUB2_BSUB_BLOCK was exiting in the middle of integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4840 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 19:57:20 +00:00
526ae92093
Getting back to '-L unmapped':
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- basic unit tests for interval sorting and merging with mix of mapped/unmapped.
- validation to ensure that locus walkers (really all non-read walkers) blow up with a user error when -L unmapped is specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4837 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 18:24:18 +00:00
d550fdfd60
Disabling integration test to see if this restores the full test suite.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4833 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 15:27:02 +00:00
abd6ce1c77
A TiTv-free approach for cutting variants! Apparently much better than previous approach, and will work for indels and SV will truly minor modifications to the code. Will discuss with methods group on Monday.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4822 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 23:08:13 +00:00
974aaa134d
Trival fix to broken build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4820 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 13:56:03 +00:00
depristo
ebanks
hanna
kshakir
rpoplin
aaron
carneiro
chartl