d9588e6083
bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:36:12 +00:00
0721c450c2
Bug fix: single unmapped read now keeps mapping qual 0 after remapping, not 37!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1557 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:29:34 +00:00
df11618092
Set default value of useLocusIteratorByHanger to FALSE. Otherwise the -LIBH flag is useless and there'd be no wayto "unset" the 'true' value. Old version was (always) using LocusIteratorByHanger. Now default iterator is indeed LocusIteratorByState, and -LIBH will switch back to the old one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1556 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:09:09 +00:00
0df6a9da5c
-Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java".
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-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:01:40 +00:00
eeb9b6eb13
GenotypeLikelhoods now support a cache per subclass, avoiding genotyping clashes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1554 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 10:39:14 +00:00
0cc219c0df
-Added unit test for walkers dealing with intervals for cleaning
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-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been. Hooray for unit tests!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 02:35:17 +00:00
ec0f6f23c7
LocusIterationByState is now the system deafult. Fixed Aaron's build problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1552 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 01:28:05 +00:00
ea6ffd3796
initial VariantEvalWalker test. More to be added soon...
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Also fixed the case where MD5 sums had leading zero's clipped off
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1551 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 01:02:04 +00:00
adce3bd536
My reference implementation is now generating a BWT which matches BWT-SW's.
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Note to self: never give project status in an svn log.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1550 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 22:11:03 +00:00
f22f590192
Successfully writing .sa files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1549 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 17:34:34 +00:00
600c234643
Starting code on phasing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1548 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 15:20:38 +00:00
3276e01e5f
fixing the build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1546 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 13:13:55 +00:00
f963cfcb21
Made enum listing header fields public.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1545 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 06:12:59 +00:00
fd20f5c2e8
For a file or files backed by a ROD implementing AllelicVariant, outputs a VCF file summarizing the information. Metadata like Hapmap and dbSNP membership, genotype LOD, read depth, etc, are annotated appropriately. The results output by this program are equivalent to those given by Gelis2PopSNPs.py.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1544 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 06:12:18 +00:00
4a95f2181d
print out the right variant
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1543 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 01:37:35 +00:00
5791da17ae
Updated to reference HLA database of unique 4 digit alleles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1542 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-07 22:12:56 +00:00
5dbba6711c
Lots of changes: (I'll send email out in a sec)
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1) Moved various disparate concordance / set splitting functionalities to a new parent tool which works like VariantFiltration (i.e. people can write various modules that fit inside and can be run though it).
2) Fixed up argument parsing in VariantFiltration to use key=value format so we don't accidentally mox up values (like I had been doing).
3) Have indel rod print samples
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1540 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-07 01:12:09 +00:00
1c3d67f0f3
Improvements to the CountCovariates and TableRecablirator, as well as regression tests for SLX and 454 data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1539 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 22:26:57 +00:00
2b0d1c52b2
General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1538 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 19:13:37 +00:00
471ca8201e
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1537 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 19:12:46 +00:00
0cc634ed5d
-Renamed rodVariants to RodGeliText
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-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 18:40:43 +00:00
fd1c72c151
Fixed package name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1535 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 15:40:06 +00:00
6c476514f8
Moved to core. Wiki pages are going up; unit tests will be written soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1533 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 15:09:11 +00:00
42c71b4382
Fix for Kris: now SNPs aren't masked by default (only when they come from a mask rod) and we can design Sequenom validation assays for them.
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I'll move this all to core in a bit...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1532 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 14:52:06 +00:00
849dce799d
This rod was all wrong for generating the alternate snp alleles (it returned null or even the wrong value); fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1531 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 14:21:46 +00:00
a08c68362e
Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 12:39:06 +00:00
3c2ae55859
changes for the genotype overhaul. Lots of changes focusing on the output side, from single sample genotyper to the output file formats like GLF and geli. Of note the genotype formats are still emitting posteriors as likelihoods; this is the way we've been doing it but it may change soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1529 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 05:31:15 +00:00
2241173fff
In order to help learn python, I decided to convert Michael's DoC python script to Java; the CoverageHistogram now spits out standard deviations for a good Gaussian fit.
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This code eventually needs to end up in the VariantFiltration system - when we are ready to parameterize on the fly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1528 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 02:23:57 +00:00
544900aa99
Migration of some core calculations (log-likelihood probabilties, etc.) from CoverageAndPowerWalker into static methods in PoolUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1527 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 21:43:29 +00:00
93cedf4285
---------------
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| Added items |
---------------
@/varianteval/PoolAnalysis
Interface to identify variant analyses that are pool-specific.
@/varianteval/BasicPoolVariantAnalysis
Nearly the same as BasicVariantAnalysis with the addition of a protected integer (numIndividualsInPool)
which holds the pool size. One soulcrushing change is that "protected String filename" needed to
become "protected String[] filename" since now multiple truth files may be looked at. It was tempting
to make the change in BasicVariantAnalysis with some default methods that would maintain usability of
the remainder of the VariantAnalysis objects, but I decided to hold off. We can always merge these
together later.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1526 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 21:26:04 +00:00
ee06c7f29f
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1525 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 19:41:12 +00:00
043c97eede
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1524 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 19:34:42 +00:00
c849282e44
reverting the HLA walker changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1523 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 19:11:57 +00:00
5202d959bf
NM attribute changed in sam jdk (?) from Integer to Short, or maybe it is presented differently by the reader depending on whether SAM or BAM is processed; in any case, both Integer and Short are safe now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1522 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 19:03:32 +00:00
ada4c5a13c
Small change to debug printing code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1521 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 18:31:21 +00:00
c3aaca1262
Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1520 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 17:20:16 +00:00
499b3536a4
Changed to use AlignmentUtils.isReadUnmapped() for better consistency with SAM spec; also, it is now explicitly enforced that unmapped reads have <NO_...> values set for ref contig and start upon "remapping"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1519 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 16:45:07 +00:00
5bd99fc1c4
VariantFiltration moved to core.
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Another win for the team.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1517 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 15:41:41 +00:00
5130ca9b94
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1516 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 15:17:02 +00:00
bdd0a6f9fa
change to make build work
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1511 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 13:43:10 +00:00
b01ac9de0c
High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1510 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 03:06:25 +00:00
e2780c17af
Checkin of the Multi-Sample SNP caller.
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Doesn't work yet; same command I used to use now causes GATK to throw an exception.
Will check with Matt & Aaron tomorrow, then do a regression test.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1509 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 00:23:28 +00:00
e2a79c5cd9
Checkpoint. The BWT that we generate now matches the first 16% of the BWT that BWT-SW generates. Cleaned up output streams to separate the byte packing / word packing from the data structure generation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1508 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 22:18:17 +00:00
3dfc77dc89
Add an indel rod which represents the initial point of the indel only
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(useful for alternate reference making)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1507 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 19:32:29 +00:00
58debd7e56
A convenience shortcut isReadUnmapped() added: thanks to SAM format specification, 'read unmapped' flag is not always required to be set for an unmapped read; this method checks both the flag and the alignment reference index/start (if those are set to '*' the flag is not required according to the spec!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1506 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 17:00:39 +00:00
0e6feff8f2
fixed locus pile-up limiting problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1505 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 16:56:44 +00:00
d8aff9a925
Bug fixes. Was ignoring the '$' character in a few places where I shouldn't have been.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1504 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 16:27:31 +00:00
55013eff78
Re-revert back to point estimation for now. We need to do this right, just not yet.
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Also, it's safer to let colt do the log factorial calculations for us.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1503 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 15:33:18 +00:00
1ada085970
Cruddy implementation of BWT creation, for understanding and testing purposes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1501 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 02:16:56 +00:00
24d809133d
Oops - comment out the printouts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1500 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 01:45:56 +00:00
depristo
asivache
aaron
ebanks
hanna
sjia
kiran
chartl
jmaguire