0d890e1bf0
Rework Eric's output management code given that the behavior of the UG changes drastically
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depending on its output format. Current implementation is probably a bit overkill-ish and
we can whittle this down to what's absolutely necessary.
Writing VCFs to the 'out' protected printstream may not work at this moment.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2425 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-22 00:33:43 +00:00
f448a263e9
The cleaner now cleans duplicate reads (instead of ignoring them) - although it doesn't include them for scoring ref or alt consenses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2424 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 21:01:55 +00:00
cf303810d3
VCF reader now creates the correct type of header line for each header type
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2423 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 20:39:06 +00:00
e06dfe44c4
Check for null platform (even when the read group isn't null) and assign it the default platform if it is
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2420 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 07:01:41 +00:00
87e5a41964
Fixed a bug that accounted for a bunch of my remaining mis-cleaned indels.
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Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2419 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 05:46:16 +00:00
b780ffb34a
Add a getFormat() method to get the output format from the writer. The need for
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this call suggests that I may be thinking about the typing of the GenotypeWriter object the wrong way.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2418 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 01:46:26 +00:00
11cbfcec9c
Get rid of backlink from ArgumentDefinitions to ArgumentSources. This will help in the future with multiple
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source -> single definition mapping sets.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2417 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-21 00:39:36 +00:00
9e53c06328
First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2416 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 19:19:23 +00:00
4ff61097cf
Trivial change: < -> <=
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2415 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 03:35:27 +00:00
566b556b50
Give user ability to turn off max allowed interval size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2414 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 03:20:22 +00:00
a5f75cbfd4
The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2413 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-20 02:34:41 +00:00
ee8bcdc61d
PooledConcordance calculations have been reformatted and bugs fixed. Now properly handles monomorphic sites. Also works with -G option now, correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2412 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-19 23:22:36 +00:00
9bf2d12c64
Misc. improvements to the LMW code. Support for emitting all sites, regardless of genotype. Min and max quality scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2411 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-19 23:20:57 +00:00
7e0f69dab5
Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2410 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 22:54:56 +00:00
80b3eb85fa
Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2409 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 22:52:44 +00:00
fdf542c214
The CycleCovariate for 454 data is now the TACG flow cycle. That is, each flow grabs all the T's, A's, C's, and G's in order in a single cycle. This is changed from incrementing the cycle whenever there is a discontinuous nucleotide along the direction of the read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2408 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 22:39:51 +00:00
c39675d2c1
VCFTool.java got left off of the last commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2407 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 21:33:53 +00:00
4ea31fd949
Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2406 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 19:16:41 +00:00
eeddf0d08e
Adding sample utils for convenience methods to pull out samples from e.g. SAMFileHeader or Genotype objects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2405 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 18:51:21 +00:00
79b997f43d
Minor fix to getValue (thanks Ryan!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2404 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:45:51 +00:00
9971a8da9a
adding a check to the RodVCF to ensure that records are in-order in the underlying VCF file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2403 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:24:45 +00:00
38563bbc2d
The values used to be integers (-1 for unpaired, 0 for unmapped, 1 for first, 2 for second); but i switched to strings before commit so it was more clear. Forgot to update the OTHER getValue method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2402 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:05:14 +00:00
7b5e332ff3
Added - PairedQualityScoreCountsWalker: counts quality scores (e.g. as a histogram) on first reads of a pair and second reads of a pair. Turns out there's a consistent difference in quality scores; even after recalibrating without the pair ordering as a covariate (there's a bit of averaging -- but not as much as I initially thought).
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Added - A paired read order covariate to use with recalibration. Currently experimental: for instance, what's a proper pair versus just a pair? Nobody should use this one...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2401 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 15:01:01 +00:00
4f59bfd513
Updates to the various GenotypeWriters to make them do simple things like write records (plus allow GLFReader to close).
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Adding first pass of stub and storage classes for the GenotypeWriters so that UG can be parallelizable. Not hooked up yet, so UG is unchanged.
The mergeInto() code in the storage class is ugly, but it's all Tribble's fault. We can clean it up later if this whole thing works.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2400 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 07:20:23 +00:00
1cde4161b7
Fixed another test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2399 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 05:05:03 +00:00
94f5edb68a
1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString)
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2. isNoCall() added to Genotype interface so that we can distinguish between ref and no calls (all we had before was isVariant())
3. Added Hardy-Weinberg annotation; still experimental - not working yet so don't use it.
4. Move 'output type' argument out of the UnifiedArgumentCollection and into the UnifiedGenotyper, in preparation for parallelization.
5. Improved some of the UG integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2398 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 04:14:14 +00:00
98839193b7
compatibility with VCF lib's switch to GenomeLoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2397 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 00:52:48 +00:00
8787dd4c5e
Various and sundry additions to VCF tools. Some useful to the general public, some one-offs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2396 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-18 00:35:45 +00:00
6fbf77be95
Updating the two solid_recal_mode options to also change the previous base since solid aligner prefers single color mismatch alignments over true SNP alignments. COUNT_AS_MISMATCH mode has been removed completely. The default mode is now SET_Q_ZERO.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2394 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 20:07:26 +00:00
07f1859290
Added integration test for running the recalibrator with no index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2393 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 19:10:53 +00:00
c75ec67f84
When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2392 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 19:01:08 +00:00
aa86f3710d
Updating HomopolymerCovariate to only count the consecutive previous bases. I left in the code but commented out for if somebody wants to worry about carry forward homopolymer problems.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2391 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 18:25:09 +00:00
b863fffdf6
Fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2390 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 17:55:00 +00:00
9143822822
Fix half-hearted attempt to try to move classes from package to package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2389 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 17:41:42 +00:00
e6cc7dab26
fixing md5 sum; new version of IndelIntervalWalker does the right thing...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2388 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 01:04:13 +00:00
acb4d477da
sync...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2387 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 01:03:01 +00:00
ba86508854
remove debug print command
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2386 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-17 00:00:01 +00:00
d72d332239
1) changed to search specifically for D and I cigar elements (and to process properly/ignore H,S,P elements) and print out only intervals that encompass actual indels. There's still one interval per read (at most) generated, which is the smallest intervals that covers ALL indels (D or I elements) present in the read; 2) if an interval (thus the original read itself and indels in it) sticks beyond the end of the chromosome, the read is ignored and this interval is NOT printed into the output; instead, a warning is printed to STDOUT (should we send it to logger.warn() instead?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2385 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 23:29:07 +00:00
5b78354efd
Fixed NPE in index check with RefWalkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2384 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 22:37:45 +00:00
e6127cd6c5
Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single
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shard for cases when the index file isn't available. Works for the case in question, but is not
guaranteed to work in general. Will be replaced once the new sharding system comes online.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2383 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:55:42 +00:00
bef1c50b3b
Some cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2382 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:41:06 +00:00
bb92e31118
Optimizations:
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1. push the ReadBackedPileup filtering up into the ReadFilters for read-based filters
2. stop querying the cigar for its length (just do it once)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2381 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:39:58 +00:00
36875fca89
Update documentation in the new help system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2380 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:33:12 +00:00
ee47eb4367
Make filters used available to the walker via getToolkit().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2379 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:26:04 +00:00
b626fc0684
Joint Estimate is now the default calculation model.
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Reworked all of the integration tests so that they're now more comprehensive, cover more of what we wan to test, and don't take forever to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2376 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 19:41:02 +00:00
e051311e8c
Added convenience methods in RodVCF to pull out all of the VCF data from the VCFRecord (e.g. getID(), getSamples(), getInfoValues())
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2374 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 17:58:41 +00:00
bb312814a2
UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).
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Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 17:28:09 +00:00
af440943a4
Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek().
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Changed peek() to element() to be consistant with the Java standards of the Queue and Stack classes (element() throws an exception if a record isn't available).
Also updated some of the ROD iterator next() methods to throw NoSuchElementException if next() is called when a record isn't available.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2372 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 23:04:40 +00:00
1035abc85f
Add minimum base quality thresholding to depth of coverage via getBaseAndMappingFilteredPileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2371 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 22:58:30 +00:00
2deae95df9
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2370 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 21:31:47 +00:00
555976d575
One more walker with formatting to fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2369 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 21:23:13 +00:00
cf46472419
Fix up Sherman's new docs in compliance with javadoc specs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2368 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 21:20:38 +00:00
df79ed8db1
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2367 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:53:41 +00:00
a80a5f1036
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2366 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:52:08 +00:00
18f61d2586
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2365 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:45:19 +00:00
5974c42468
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2364 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:41:35 +00:00
d8cfd707bc
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2363 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:35:18 +00:00
4322beeb35
Updated documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2362 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:33:38 +00:00
4148991d81
Now also encodes amino acids, includes documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2361 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 20:26:56 +00:00
9b0bdbbf29
Fix for homopolymer bug: ref was lowercase, alt allele was uppercase, so alt != ref. Yuck.
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This is a temporary fix - pushed more elegant solution over to Matt.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2360 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 19:02:23 +00:00
a810586418
Check-in without javadoc = smackdown
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2359 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 15:32:39 +00:00
b234019cf5
Readded locus printing suppression to DoC walker
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(and removed unused import from UG)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2358 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 14:50:56 +00:00
0d2a761460
Bugfix for minBaseQuality to ignore deletion reads. LocusMismatch walker now allows us to skip every nths eligable site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2357 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 14:38:39 +00:00
bf7bab754e
Made getPileupWithoutMappingQualityZeroReads() and getPileupWithoutDeletions() more efficient, per Mark's cue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2356 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 04:35:21 +00:00
874552ff75
Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper.
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[Also, enable Mark's new UG arguments]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2355 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 04:29:28 +00:00
2cbc85cc7a
min mapping quality and min base quality arguments for UG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2354 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 03:57:27 +00:00
faa638532a
Correct location
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2353 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 02:42:21 +00:00
1da97ebb85
Walker for calculating non-independent base errors, v1. Will be moved to somewhere not in core
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2352 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-15 02:40:15 +00:00
1389ac6bdf
Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg.
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Will fix again.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2351 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 22:42:50 +00:00
b42fc905e8
Added - new tests (Hapmap was re-added)
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Modified - Hapmap now takes a -q command to filter out variants by quality
Modified - MathUtils - cumBinomialProbLog now uses BigDecimal to handle some numerical imprecisions
Modified - PowerBelowFrequency - returns 0.0 if called with a negative number (can't be done from inside the walker itself, but since it's called elsewhere one can't be too careful)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2350 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 21:57:20 +00:00
8e44bfd2ef
CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2349 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 21:52:30 +00:00
c7b23d6ca5
Now that VCFGenotypeRecords implement SampleBacked (as they should), a quick fix was needed to get the GenotypeConcordance working when no direct samples were provided in a samples file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2348 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 04:27:16 +00:00
bd7b07f3f1
added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2347 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-14 00:15:44 +00:00
97618663ef
Refactored and generalized the VCF header info code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2346 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 21:02:45 +00:00
05b8782d5f
Documentation updates. Moved CountX.java walkers to QC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2345 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 18:40:22 +00:00
92307361a4
In preparation for move
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2344 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 18:28:06 +00:00
45199136f0
Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2342 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 04:13:30 +00:00
bd2a46ab4c
I want to move over to hpprojects tonight, so I'm checking in various changes all in one go:
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1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis).
2. Move error checking code from rodVCF to VCFRecord.
3. More improvements to SNP Genotype callset concordance.
4. Fixed some comments in Variation/Genotype
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-13 02:52:18 +00:00
2748eb60e1
Added short documentation for each class so that it appears in the walker command-line documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2340 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 21:41:07 +00:00
78e94b5a84
TableRecalibration now puts the full list of walker arguments into the PG tag of the bam file it creates. Thanks Matt and Eric. Also, the default nback for the HomopolymerCovariate is 8, down from 10.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2339 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 17:29:41 +00:00
014013630f
Added hieracrchy to the covariate classes: Required, Standard, and Experimental. Required covariates (rg and reported quality) are added for the user whether or not they are specified in the -cov list. There is now a -standard option in CountCovariates which will add in all of the standard covariates so the user doesn't have to type them all out or even know which ones are the standard. There is logger output to say which covariates are being used of course. The list of covariates used is also added to the PG tag in the bam file produced by TableRecalibration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2338 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 16:34:05 +00:00
6955b5bf53
Cleanup of the doc system, and introduce Kiran's concept of a detailed summary
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below the specific command-line arguments for the walker. Also introduced
@help.summary to override summary descriptions if required.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2337 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-12 04:04:37 +00:00
cdfe204d19
Incorporated feedback from Kiran. Use the Javadoc first sentence extraction capability to just show the first sentence from each line of Javadoc. @help.description can still be used to produce exceptionally verbose descriptions.
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Also increased the line width as much as I could tolerate (100 characters -> 120 characters).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2336 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 21:59:55 +00:00
4fa4e95fbc
Updated AnalyzeCovariates to extend org.broadinstitute.sting.utils.cmdLine.CommandLineProgram and use the standard argument parsing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2335 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 21:57:18 +00:00
38d9f7b903
Renamed ReferenceContext's getSimpleBase() method to getBaseIndex()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2334 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 20:14:39 +00:00
09811b9f34
Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2333 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:51:05 +00:00
0da2105e3c
Moving DuplicateQualsWalker to oneoffprojects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2332 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:22:32 +00:00
60c3eb4b60
Added help.description to the recalibration walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2331 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:02:29 +00:00
2ea7632b76
The SNP genotype concordance module is now more comprehensive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2330 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:34:33 +00:00
590aeee7d2
Documentation for more basic walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2329 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:15:40 +00:00
d1815f3559
More documentation for walkers that I'm familiar with in the collection of core walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2328 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:02:33 +00:00
956c36a2c8
Help for the qc package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2327 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:32:47 +00:00
450ea233a5
Docs for the basic walkers: CountLoci, CountReads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2326 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:17:34 +00:00
f97ac939fa
Punch up the help documentation for CombineDuplicates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2325 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:09:35 +00:00
86dc98bfb5
update the documentation for CombineDuplicates for the new help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2324 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 17:01:42 +00:00
420725441a
documentation updates for the new help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2323 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 16:15:44 +00:00
23d96b1d43
Help system content for the alignment module.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2322 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 16:01:25 +00:00
2de7e1a178
Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.
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The only major difference is that we are now able to get accurate allele balance ratios.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2321 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 05:28:28 +00:00
8f7554d44f
A few improvements to pooled concordance calcluations. Now will show you FN with the -V option. BasicGenotype now prints out a reasonable representaiton wiwth toString
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2320 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 23:09:10 +00:00
f64a4c66ac
some tweaks for the GATK paper genotyper to better work with shared memory parallelization, added documentation changes for Matt's new help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2319 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 22:33:51 +00:00
a7cd172628
Added 8x coverage field and minimum base quality command line option in order to be able to compare to U. Wash. exome metrics.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2318 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 22:14:44 +00:00
2869270c11
Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2315 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 21:11:42 +00:00
31b1d60d28
Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2314 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:50:06 +00:00
0c396f04a2
Fix obvious cut/paste error in output stream management code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2313 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:23:13 +00:00
11ac7885b0
Pull out StratifiedAlignmentContext code so other walkers can use it.
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This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2312 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:21:16 +00:00
adb2fdbee7
Before, we were only checking that the reference was present if @Requires required that a reference was present. Now we always check that a reference is present, so that we get an intelligent error message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2311 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 19:15:48 +00:00
5eac510b2f
Refactor the code I gave Eric yesterday to output command line arguments.
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Convert it from a completely wonky solution to a slightly less wonky solution
that will work in more cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2310 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 18:57:54 +00:00
74b8055b6a
Only show extra walker help if the user didn't specify a walker or specified
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an invalid walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2309 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 16:43:06 +00:00
e6f541fdca
Forgot to update integration test last night
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2308 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 12:57:10 +00:00
0fae798b3a
1. Discoverable base calculations don't care about Genotypes (use Variation's PError regardless of whether the call is ref or var - it's the correct value even for ref calls).
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2. Call a base genotypable if any of the Genotypes is above the threshold (you can't assume there's a single Genotype associated with the Variation).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2306 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 04:26:06 +00:00
a45adadf1f
VCFGenotypeRecord already defines all the methods needed to be SampleBacked, so let's annotate it as being SampleBacked. This way, when used as a generic Genotype, sample data can be retrieved.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2305 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 04:16:21 +00:00
78d5ac9bc2
Don't check het count when there are multiple Genotypes per Variation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2304 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 04:07:47 +00:00
ee691b8899
Added a whole bunch of unit tests for VCF reading.
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We could still use more, but this is a good start.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2303 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 03:31:23 +00:00
f7c44ad019
- Read in arguments for the header based on reflection
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- Hook up Variation and Genotype in SSG
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 21:35:33 +00:00
408f6f3dee
Refactoring of prior commit: better handling of unnamed package within the help system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2297 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 20:12:35 +00:00
1d2151adcf
Better handling of nulls output by
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2296 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 19:34:56 +00:00
40c2d7a4bc
Fix all-bases-mode and genotype-mode in the UG and add integration tests for them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2295 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 17:41:30 +00:00
4e54b91ce4
UG now outputs the FORMAT header fields when there's genotype data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2294 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 16:31:07 +00:00
12c49ea485
Added DuplicateReadFilter to filter out reads that are marked as duplicates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2293 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 15:42:53 +00:00
fb900b12e1
VariantFiltration now details the filters it has used in the header of the VCF it produces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2292 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 15:36:15 +00:00
7a76e13459
Better explanation in the exception being thrown.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2291 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:59:36 +00:00
8d67d9ade3
-Minor fix in UG for all-bases mode
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-Make minConfidenceScore in VariantEval a double so non-integer values can be used (requested by Steve H).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2290 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:49:10 +00:00
8a1c876104
Weird. I thought I had updated these md5s...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2289 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:31:41 +00:00
717eb1de96
- Depth annotation now includes MQ0 reads
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- Removed MQ0 annotation
- Updated RMS MQ annotation to use new pileup
- UG now outputs all of its arguments as key/value pairs in the header (for VCF)
- Cleaned up VCFGenotypeWriterAdapter interface a bit
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 02:53:00 +00:00
e8822a3fb4
Stage 3 of Variation refactoring:
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We are now VCF3.3 compliant.
(Only a few more stages left. Sigh.)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2287 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-08 21:43:28 +00:00
9e2f831206
A bit of cleanup in preparation for Picard patch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2286 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-08 16:09:04 +00:00
d3b78338da
Get rid of characters in the docs that aren't universally compatible with
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character sets used throughout the group.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2285 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:41:07 +00:00
d75d3a361a
Clean up some of the walker help output based on additional experience and
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feedback received. Also, add a flag to build.xml to disable generation of
docs on demand (use ant -Ddisable.doc=true to disable docs).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2284 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 21:33:11 +00:00
a3e88c0b1c
Cleanup results of bad merge.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2281 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:30:49 +00:00
10be5a5de9
Move some files around to reflect our growing help infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2280 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:23:12 +00:00
1d5b9883db
Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2276 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 14:26:27 +00:00
8f461d3c40
Critical bug fix for VariantEval dbSNP calculations. Moved the system over to the new improved ROD iterators, resulting in dbSNP rates jumping 5% or so, due to masking of true SNPs by preceding indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2274 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 03:36:38 +00:00
8089aa3c50
Adding support to override the help text.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2273 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 00:16:26 +00:00
c0528cd88e
Updated the CallsetConcordance classes to use new VCF Variation code... and uncovered a whole bunch of VCF bugs in the process. I'm not convinced that I got them all, so I'll unit test like crazy when the refactoring is done.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2272 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 11:43:40 +00:00
b6f8e33f4c
Stage 2 of Variation refactoring:
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VCFRecord now implements Variation, VCFGenotypeRecord now implements Genotype.
Because of this change, RodVCF is now just a wrapper around the VCFRecord and does nothing else. Also, one can call toVariation on the VCFGenotypeRecord and it returns the VCFRecord.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2271 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 06:48:03 +00:00
3b440e0dbc
Add a taglet to allow users to override the display name in command-line help.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2270 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 04:12:10 +00:00
08f2214f14
Stage 1 of massive Variation/Genotype refactoring.
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This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers. I haven't finished refactoring the writers and haven't even touched the readers at all.
The major changes here are that
1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes
2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called).
The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 03:12:41 +00:00
b04de77952
First pass at a reorganized walker info display. Groups walkers by package
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and displays walker data extracted from the JavaDoc. Needs a bit of help,
both in content and flexibility of package naming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2267 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 23:24:29 +00:00
07b88621c5
Improved RankSum calculations and RankSum annotation. Much more meaningful
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2266 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 22:16:40 +00:00
4c147329a9
Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
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in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 20:08:41 +00:00
1e8dcc30da
-dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data
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-added code to cache the allele list so it didn't need to get recomputed each time it was requested.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2260 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 14:56:48 +00:00
58937bf9ba
You can now use the -exp flag to tell the Genotyper to include experimental annotations when it calls out to VariantAnnotator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2256 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 04:45:05 +00:00
b05e73a914
Finished implementation of the Wilcoxon Rank Sum Test thanks to Tim Fennell (calculating the normal approximation) and Nick Patterson (dithering to break tie bands).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2255 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 04:04:39 +00:00
861221d046
- Moved various header line printing into a single method
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- Fixed output for coverage above min depth
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2254 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 02:15:43 +00:00
aef4be5610
Moved CoarseCoverageWalker to core and packaged both coverage walkers in coverage/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2249 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:53:36 +00:00
df4e001a07
Renamed to more accurately describe its function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2248 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:34:49 +00:00
c2017cc91b
PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2247 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:23:59 +00:00
01cf5cc741
1. Merged CoverageHistogram into DepthOfCoverageWalker
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2. Fixed bug in histogram calculation for small intervals
3. Better output in DoCWalker
4. Comments added to code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2245 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:01:53 +00:00
44b9f60735
PercentOfBasesCovered functionality moved to DepthOfCoverageWalker. Added integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2244 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 16:11:09 +00:00
126d1eca35
Move to core (qc/)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2243 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 15:45:58 +00:00
9da5cc25ad
More archiving (with permission from Andrey) plus a move to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 15:40:27 +00:00
b3bdcd0e60
make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2241 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 06:59:27 +00:00
a88202c3f6
Refactored DoCWalker to output in a more helpful and usable style. It now outputs in tabular format with 2 different sections: per locus and then per interval.
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I am now at a point where I can merge the functionality from other coverage walkers into this one.
Thanks to Andrew for input.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2239 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 05:28:21 +00:00
d7e4cd4c82
Moving some useful and stable walkers to core:
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- ClipReads
- PrintRODs (generalized to print all RODs that are Variations)
- FixBAMSortOrderTag (added documentation to walker so that people know what it does and why)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2238 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 03:00:45 +00:00
46f3d3e39b
Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2233 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:15:52 +00:00
451a20ed55
commenting out some broken integration tests, to be uncommented if needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2232 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:13:24 +00:00
c776f9fb90
Simple utilities for dealing with Complete Genomics data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2230 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 22:51:41 +00:00
9d598f1c82
some integration test clean-up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2229 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 21:11:02 +00:00
a09fee2b5e
Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2228 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:28:07 +00:00
dec0a781c2
Un-reinventing the wheel. --sleep argument removed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2227 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:19:28 +00:00
a3343c75db
Move and rename a hybrid-selection-specific coverage calculation to hybridselection/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2225 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:11:22 +00:00
2c83f2f2bc
Move MSG - plus now obsolete classes which it depends on -- to oneoffprojects (with permission from Jared).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2224 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 20:04:22 +00:00
6a9e7bea05
Removing experimental annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2220 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:03:55 +00:00
c180a76b05
Added option "append": if set, and the specified discovery output already exists, don't re-call anything that's already present in that file. Append new calls to it.
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Great for resuming long jobs that died partway through.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2219 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 18:56:19 +00:00
0a2304eff8
- Rename minConfidenceScore in VariantEval to minPhredConfidenceScore
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- Moved validation walkers to new qc dir
- Killed unused test
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:59:19 +00:00
a5dfc9107d
- Cleaned up annotation code some more
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- Use QualityUtils when phred-scaling now
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2217 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:45:29 +00:00
7055a3ea2d
- All annotations are now required to return their VCF INFO keys and descriptions
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- Renamed keys to fit with the standard naming
- FisherStrand is no longer standard
- Integration tests no longer test experimental annotations since they're not stable
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:24:06 +00:00
67179e2412
Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:47:35 +00:00
2838629724
-VCF writer now checks whether the allele frequency has been set before trying to write it out.
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-Renamed methods to be more consistent.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:25:32 +00:00
6231637615
fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2213 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 15:41:35 +00:00
d487428468
remove incorrect parentheses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2211 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 06:46:32 +00:00
886c44303a
-Removing BTTJ integration test -- this broke a few revisions ago (2169) and it is unclear whether the resulting change was a correction to something that had previously been incorrect, or a true build-breaker. I'm currently investigating which case this is, but since Bamboo is back up I'm removing this _temporarily_ so that other testing can occur, and will make whatever changes to the test necessary to reflect the truth, then replace the test itself. Additional (and related) pileup tests are upcoming as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2210 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 05:37:15 +00:00
b979bd2ced
- Optimized implementation of -byReadGroup in DoCWalker
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- Added implementation of -bySample in DoCWalker
- Removed CoverageBySample and added a watered down version to the examples directory
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2209 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 03:39:24 +00:00
7c73496e72
Moved DoC walker over to new pileup system so it no longer moves like it's stuck in molasses.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2208 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 02:46:39 +00:00
ba8a8febc6
Thanks to Steve Hershman for finding this bug:
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getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled). Probably we should change the method to be getNeg10Log10PError(). Anyone have strong feelings on this?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 01:59:03 +00:00
3303808a8f
Yet more walkers moved to oneoffprojects.
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Made hybridselection subdir in playground.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2205 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 21:29:12 +00:00
05923f7fba
Started transition to oneoffprojects.
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Moved/killed a few other walkers (with permission).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2204 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 21:19:02 +00:00
c36069355e
Trivial change to verbose
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2203 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 20:48:10 +00:00
74f6526e09
VCFHomogenizer: A class that extends InputStream and dynamically re-writes pilot1 VCF's to be on-spec.
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VCFTool: A command-line tool with various useful VCF functions (validate, grep, concordance).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2202 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 17:55:42 +00:00
adf8f1f8b3
Add an InputStream constructor, which is immensely useful for various reasons.
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Also a minor performance optimization.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2201 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 17:25:00 +00:00
e581cceab6
Got Kris's permission to delete these walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2200 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 16:57:28 +00:00
3180fffd43
Eliminated unnecessary boxing of longs in RecalDatum. Changes to RecalDatum in preparation for new AnalyzeCovariates script. Updated TableRecalibrationWalker to make use of these changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2199 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 16:49:05 +00:00
21a9a717e4
Some minor changes and test:
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- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
- VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
- A PileupWalker integration test on a particularly nasty FHS site
- Two second-base annotation related integration tests on that same site
+ outputs were all hand-validated in matlab; within a certain tolerance for the annotations
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 15:15:54 +00:00
084337087e
Removing deprecated code and walkers for which I had the green light from repository.
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Moved piecemealannotator and secondarybases to archive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2195 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 05:58:20 +00:00
2c16c18a04
Move Andrey's old indel code (plus MSG accuracy test, which depends on it) to archive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2194 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 05:29:00 +00:00
7c6c490652
An unfinished implementation of the Wilcoxon rank sum test and a variant annotation that uses it. I need to merge and update this code with Tim's implementation somehow - but that won't happen until later this week, so I'm committing this before I accidentally blow it away.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2193 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 04:56:17 +00:00
00f15ea909
Improved performance of deletion-free pileup and added mapping-quality-zero-free pileup convenience method.
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Finished converting genotyper and annotator code to new ReadBackedPileup system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2192 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 04:50:47 +00:00
6bb864da2a
More misc cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2191 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 22:29:07 +00:00
b89b9adb2c
misc code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2190 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 21:16:00 +00:00
e793e62fc9
minor code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2189 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:57:20 +00:00
4969cb1957
CountCovariates uses new optimized ReadBackedPileup. It also smarter about re-doing calculations for the dnsnp variation rate sanity check.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2188 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:35:40 +00:00
add2fa7ab4
more use of new ReadBackedPileup optimizations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2187 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 20:04:01 +00:00
817e2cb8c5
Recalibrator makes use of the new GATKSAMRecord wrapper and now no longer has to hash the SAMRecord. Covariate's getValue method signature has changed to take the SAMRecord instead of the ReadHashDatum. ReadHashDatum removed completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2185 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 19:59:17 +00:00
e9a8156cfb
Use new optimized ReadBackedPileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2184 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 18:17:18 +00:00
d8146ab23d
Changed the format of the recalibration csv file slightly so that it is easier to load the file into something like R and look at the values of the covariates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2183 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 17:55:23 +00:00
a184d28ce9
Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine.
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I note that all integration/unit tests pass except for BaseTransitionTableCalculatorJava, which is already broken.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2182 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 17:39:29 +00:00
af22ca1b47
Bug fixes for VariantEval. dbCoverage now reports dbSNP rate, not some wierd eval_snps_in_db as before. We now separate non-indel and non-snp db sites in dbcoverage. Some dbSNP records don't fit into these two categories. Also fixed a consistency issue where novel / known sites where being determined solely by whether dbSNP had a record there, rather than the stricter dbcoverage screen for isSNP().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2180 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 01:39:01 +00:00
27651d8dc2
Oops. numReads is now called size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2175 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 06:59:17 +00:00
21744e024b
Quick walker that determines % of bases covered at (user - defined depth)x . I've been maintaining it in my directories alone, but now that i've accidentally deleted it twice, into playground it goes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2174 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-29 06:51:19 +00:00
3300ca906a
An iterator for Eric to use when injecting his new wrapping reads -- a stopgap solution for getting additional caching
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functionality into a SAMRecord.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2173 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-27 22:25:52 +00:00
hanna
ebanks
depristo
aaron
rpoplin
chartl
jmaguire
asivache
andrewk
sjia
kiran