7af0532292
An attempt to have more intelligent sorting of RODs. Tested with maf only so far. Should be able to reference-sort dbsnp, bed and vcf as well, bugs nonwithstanding. Very simple, brute-force implementation using SortingCollection. Should I have used tribble indexing machinery instead?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5118 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 22:10:07 +00:00
fa8963522b
Ignore header line if it happens to be passed to the codec again, instead of crashing on it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5116 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 21:44:33 +00:00
8d389e149f
Now can deal with input files that contain multiple copies of the same event. Only one assay sequence will be designed for each distinct variant, redundant variants will be discarded. Redundancy is defined as same start, same variant type, same ref and alt alleles (it does not matter, e.g., what the sample was as we do not record sample information anywhere).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5115 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 21:42:29 +00:00
f2de39d661
Calculates phase concordance rates between trio and RBP-phasing tracks, stratified by trio status (Het3, non-Het3)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5114 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 20:50:01 +00:00
ffd5f407a5
Retain only a single walker to perform calculation of haplotype extents
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5110 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 18:33:32 +00:00
2182b8c7e2
Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5108 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 15:08:21 +00:00
9cb1ae384c
Constant precision for floating point numbers. Added integration test - carries over tests from VariantEval with the necessary modifications to command-line arguments and md5s. Disabled use of 'synchronized' keyword because I clearly don't get how that keyword is supposed to work yet...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5107 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 05:19:18 +00:00
f29bb0639b
Documentation and cleanup of the distributed GATK implementation. Detailed documentation -- given that Matt will be extending the system in the near future -- about how the locking and processing trackers work. Added error trapping to note that distributed, shared-memory parallelism isn't yet implemented, instead of just not working silently. General utility function for the analysis of distributedGATK operation in the analysis directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5106 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 03:40:09 +00:00
f036a178f1
Added support for MAF features. So far works for MAF Lite only, annotated MAF is NOT TESTED yet AT ALL.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5105 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 03:20:46 +00:00
91e4bb0285
Added walker to calculate haplotype lengths for ALL fragments produced by stitching together phased sites (actually, stitching together everything BUT unphased het sites)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5104 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 03:09:20 +00:00
ac3fd567b4
Ugly one-off error fixed in building design sequences for indels: the event position is immediately *before* the event, so the ref base at the current locus is the base immediately *before* [ref/alt] element
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5103 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 02:53:03 +00:00
3e9f185dad
Fixed issue with GenotypeConcordance being initialized incorrectly when the first seen comptrack had no samples.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5102 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 01:12:27 +00:00
58f0ecff89
Fixes to support evaluations with TableType elements - each such object now gets a separate entry in the output table. Added codon degeneracy stratification. Handle null elements in reports (useful for debugging).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5101 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 22:09:59 +00:00
a264b16358
Patch from Brett (with minor tweaking by me) to expose all the relationships
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of a particular sample in hash format. Thanks, Brett!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5100 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 21:46:13 +00:00
9c728979cc
In order to calculate haplotype lengths of trio+RBP, I implemented a simple trio phaser as an option to ComparePhasingToTrioPhasingNoRecombination, which already decides if the trio could theoretically phase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5099 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 20:17:48 +00:00
5ed128f839
Slightly more tolerant timing setting. Main() method in GenomeLocProcessTracker to generating timing data for trackers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5097 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 15:16:07 +00:00
61c29d550d
Fix for NullPointer where a run starts but there's nothing to do (no shards) and reduceInit() wasn't being called correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5096 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 15:15:10 +00:00
2901299ff6
Sets the number of samples to all of the samples in the file when it's not specifed on the command-line explicitly. GenotypeConcordance no longer a standard evaluation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5094 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-27 01:38:26 +00:00
466f8f8a3c
Compares RBP phasing to a simple trio phasing model that can phase a child het iff both parental genotypes are known and at least one of them is not het [at EACH of the sites in the pair to be phased]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5092 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 23:43:29 +00:00
43812a28fc
If among all the multiple alignments for the given read we have 'unmapped' ones (can happen with bwa 0.5.7 and maybe later versions), then discard the latters and keep only the mapped ones. Keep 'unmapped' only if its the only alignment available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5090 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 20:07:08 +00:00
63b709d992
When remapping the read, set MAPQ, CIGAR etc to 0/null for unmapped reads. This is not required according to spec but current samtools jdk otherwise dies in STRICT validation mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5089 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 19:49:07 +00:00
d33162145b
Moving the --sites_only argument up into the VCFWriter itself so that any walkers that write VCFs can choose not to emit genotypes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5088 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 19:38:16 +00:00
a97184fddf
Frick! Changed to refer to the *playground* version of VariantEvaluator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5087 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 19:33:03 +00:00
a9d0772516
When evaluating JEXL expressions, on't blow up if the eval VC is null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5085 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 18:25:03 +00:00
22e599ec76
Fixed output report to properly handle evaluation modules with TableType objects. Promoted CpG to a standard stratification. Demoted Filter to a non-standard stratification. Now, if the filter stratification is not specified, VariantEval only evaluates PASSing sites.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5084 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 17:38:21 +00:00
2dcce58279
oneoffs walker to assess GLs at truth sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5083 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:59:05 +00:00
0429301536
Added ability to output just sites (no genotypes) from UG with the --sites_only argument. Note that we do still genotype in this mode so that the INFO annotations are identical, but we strip the genotypes out of the VC right before writing to output. In other words, this is not designed to make UG go faster; the point here is to allow downstream tools not to have to parse GTs if they don't want to. Here you go, Ryan.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5081 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:52:38 +00:00
01e032e89c
Missorted BAMs are User Exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5080 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:09:39 +00:00
be697d96f9
An apparently robust implementation of the file locking for distributed computation, using Lucene's file creation locking approach. It is worth trying out for those with large-scale, high-cost data sets. Details and discussion at group meeting on Wednesday. Some cleanup still needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5079 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 13:45:40 +00:00
862b299b47
Fix Picard OTF index generation issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5077 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 03:42:46 +00:00
6ac888d26a
Correct accounting for cases where first het in interval is phased
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5075 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:48:54 +00:00
af79fa629f
PROPERLY print out list of intervals and their stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5074 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:20:36 +00:00
db2e2cb0ff
Another trivial change to make VQSR work with indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5073 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 19:05:31 +00:00
17ba75e502
Can now print out list of intervals and their stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5071 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-25 18:36:59 +00:00
9db02059ac
Fix for Ryan's issue: reads ending with indel distort the location of the
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pileup, resulting a two map() calls for the same locus (and no map call for
the locus immediately following).
Fixed bug and added comprehensive unit tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5067 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-24 19:49:39 +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
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
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
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
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
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
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
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
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
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
bd2af33a16
misc clean up in VQSR
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5014 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-18 21:04:31 +00:00
00453919d2
VQSR now only uses the valid polymorphic sites for training and truth sensitivity calculations. Any number of tracks whose ROD binding begins with the name truth can be used as truth sensitivity tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5012 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-18 20:48:19 +00:00
4bec93e3e4
Permit retrieval of read names for debugging purposes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5011 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-18 16:09:34 +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
2f4a436719
Throw an exception if no eval rods are specified. If one or more samples are specified, subset the 'all' VariantContext to just the specified samples. This is useful when you want to see what effect dropping certain samples will have on the metrics and you don't want to go through SelectVariants first.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5009 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-17 06:46:10 +00:00
366c3a0b8f
Incompatible chain files are user exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5008 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-16 05:26:47 +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
579e0d59fa
Rewrote warning message to discourage use of unsafe mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5003 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 21:32:53 +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
73acfa654a
Fixed double-counting bug. Fixed issue where evaluation module with an update2() method wasn't getting called if the comp track was null. Added a column to the output report indicating the table name for easy greppability. Fixed an issue where, if sample-level stratification was not required, the sample-level VCs would be generated anyway.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5000 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 14:06:43 +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
bfbf75fe3e
Fix error in command-line validation: don't ever allow intervaled access to unindexed read stream, no
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matter what type of traversal it is.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4997 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-14 02:49:04 +00:00
00310c05bb
Fix corner condition that happens when there are indels right at the end of a contig and there's not enough reference to build a haplotype.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4996 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 21:08:22 +00:00
c0031b05ff
Stamp out lazy loading in the PluginManager. This is an attempt to stamp
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out the non-deterministic VariantEvalIntegrationTest errors we've been seeing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4995 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 20:58:28 +00:00
b107c97c1a
Cannot have "=" sign in reason, so change to ":"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4991 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 17:23:44 +00:00
b4a2112a0d
Added the "previous locus" to interesting sites VCF (locus with respect to which the site is phased)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4990 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 17:19:20 +00:00
e8f0ae4b09
Renamed and documented some phasing-specific classes to make their purpose clearer to someone browing through the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4989 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 16:17:36 +00:00
ffae7bf537
Moved phasing-specific utilities to phasing sub-directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4987 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:38:20 +00:00
91824f478e
FASTQ directory is gone
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4986 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 15:16:06 +00:00
e3956148ac
removing unused fastqtobam
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4985 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:29:32 +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
e0092bb160
Experimental feature: change the rate at which log messages appear on-the-fly
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and enable/disable performance logs from outside the JVM process. Making this
available for the moment; we'll see whether it ends up being useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4983 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 04:20:53 +00:00
9e93091e9a
-baqGOP now takes phred scaled scores instead of probabilities in the command line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4982 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 00:06:38 +00:00
5736d2e2bb
Something I should have done a long time ago: attempt to detect whitespace
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after the line continuation backslash and enhance the error message if it
appears.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4981 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 23:15:08 +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
8a6b126ea8
Several cleanups to IndelMetricsByAC:
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- No longer a standard eval module to keep integration tests happy
- Remove class name overlaps with SimpleMetricsByAC so that modules don't overwrite each other's files, and to make it easier to grep results.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4978 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 18:35:24 +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
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
bdd382198c
Necessary changes to enable HaplotypeScore annotation for indels
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4974 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 01:09:12 +00:00
23597a2bde
Variant Eval module that collects indel statistics (basic counts and event sizes) and partitions by AC (similar to SimpleMetricsByAC in the SNP case)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4973 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-12 01:08:09 +00:00
48052907a6
A hom genotype can always be considered phased
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4972 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-11 18:48:48 +00:00
c2dd956888
Moved PrintReferenceVariantsWalker to playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4971 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 22:07:41 +00:00
8ba3a5a43f
Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.
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GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines.
When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly.
Added the most basic of all example QScripts for debugging, Hello World.
Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 21:07:29 +00:00
ee348ac9d4
Add a hidden mode to the realigner to turn off SW but still use indels other than known ones (i.e. those already in the reads)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4969 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 20:27:04 +00:00
01c2091cd9
A LocusWalker to print the haploid reference genome as a VCF file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4968 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 16:59:41 +00:00
9648399630
Boneheaded silly bug in indel caller - posterior probability computation was using priors gotten from SNP heterozygosity, not indel heterozygosity. Added then indel het. argument to command line and hook it up (not a radical change in calls though, just a few dubious calls around the edges fall off)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4967 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-10 14:56:28 +00:00
b24e1134f9
unfortunately samrecord pileup also uses zero length intervals to indicate deletions; this will have to be a BED specific exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4964 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 22:32:50 +00:00
b34e2f733f
Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.
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Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 22:03:36 +00:00
60f45a7c49
Stupid me. Forgot to put this check in the last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4959 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 19:16:41 +00:00
56b87da8f9
a better error message for the situation where a RMD track generates a negitive length interval; the user will now see a message like "Bad input: A feature produced by the reference metadata track named "bed" at position chr1:10434-10433 has a start greater than the stop; this is an invalid position "
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4958 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-07 19:06:04 +00:00
asivache
fromer
depristo
kiran
hanna
ebanks
delangel
rpoplin
kshakir
carneiro
aaron