0c54aba92a
Changes:
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@VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object.
@AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones.
@ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true.
Added:
@PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls
and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-11 15:01:50 +00:00
e24c8d00d5
So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday).
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After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution. However, this shouldn't cause any short-term problems because the data truly is optional.
VF test's MD5s are updated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1580 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 14:28:43 +00:00
296878e8e3
adding a basic implementation of the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1578 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 04:41:13 +00:00
5a64a80ab5
changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 04:31:33 +00:00
c988205884
Notes for Aaron in SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1576 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 03:18:51 +00:00
1362a56227
Added fasta tests and small fix to cleaner test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 03:13:11 +00:00
8ca89279aa
Added a test for VariantFiltration and the VECs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1574 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 02:21:14 +00:00
6de54dcd2a
Higher-level readers and writers for BWTs and suffix arrays.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1573 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 22:45:32 +00:00
0093482c62
N reference base fix for SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1572 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 21:19:36 +00:00
bc9fe31cf5
Cleanup of int-packed file readers / writers. All primitive writers for BWTs and SAs are in place; time to move on to compound reader / writers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1571 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 20:36:39 +00:00
d9f3e9493f
Does not return 0-length cigar elements anymore (used to do so when previous cigar element ended exactly at the segment boundary)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1570 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 20:05:55 +00:00
cb31d5a0ab
VariantFiltration now outputs VCF. Important changes:
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1. VariantsToVCF can now be called statically to output VCF for a single ROD instance; this is temporary until we have a VCF ROD.
2. VariantFiltration now outputs only 2 files, both mandatory: all variants that pass filters in geli text, and all variants in VCF.
If there are any problems, go find Aaron.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1569 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 20:04:32 +00:00
dd0085c428
1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call)
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2) when reads with deletions are requested, adds to the pile just those: reads with 'D' over the current reference base, but not 'N'
3) next() now implements a loop: recursive forward iteration calls to next() until ref. position with non-zero coverage is encountered were OK for (short) deletions, but with long stretches of N's they end up with stack overflow
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1568 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 20:04:04 +00:00
542af6402e
output correct format for Sequenom SNPs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1567 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 19:21:53 +00:00
43d1c6741c
Cleanup. Separate common packing functionality into utils class. Make base packing utility as generic as possible.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1566 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 17:54:12 +00:00
3b1e966b4c
Lowercases the sequencing platform so that a difference in case doesn't lead to the failure to look up an entry in the hash.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1565 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 17:35:45 +00:00
d82d6c0665
Excludes variants that fall below a certain LOD that changes as a function of depth.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1564 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 17:34:16 +00:00
06eae52292
Throws an exception if you attempt to use a filter that doesn't exist.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1563 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 17:33:27 +00:00
1060b36288
Bug fix: 'N' cigar elements now treated properly; for all practical intents and purposes, N is the same as D and should be treated as such, the difference is only in logical interpretation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1562 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 17:08:35 +00:00
bed646e4f6
Adding cleaner test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1561 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 16:05:56 +00:00
9c7f456510
Changed the short name on the PoolSize cmd line argument
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1560 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:53:22 +00:00
9d69bd2c84
Modifications:
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@CoverageAndPowerWalker - removed a hanging colon that was being printed after the reference position
@VariantEvalWalker - added a command line argument for pool size for eventual use in doing pooled caller evaluations. As now, the variable is unused.
@AlignmentContext - altered the scope of class variables from private to protected in order that child objects might have access to them
New Additions:
Filtered Contexts
Sometimes we want to filter or partition reads by some aspect (quality score, read direction, current base, whatever) and use only those reads as
part of the alignment context. Prior to this I've been doing the split externally and creating a new AlignmentContext object. This new approach makes
it a bit easier, as each of these objects are children of AlignmentContext, and can be instantiated from a "raw" AlignmentContext.
@FilteredAlignmentContext is an abstract class that defines the behavior. The abstract method 'filter' is called on the input AlignmentContext, filtering
those reads and offsets by whatever you can think of. The filtered reads/offsets are then maintained in the reads and offsets fields. These classes can
be passed around as AlignmentContexts themselves. Writing a new kind of read-filtered alignment context boils down to implementing the filter method.
@ReverseReadsContext - a FilteredAlignmentContext that takes only reads in the reverse direction
@ForwardReadsContext - a FilteredAlignmentContext that takes only reads in the forward direction
@QualityScoreThresholdContext - a FilteredAlignmentContext that takes only reads above a given quality score threshold (defaults to 22 if none provided).
A unit test bamfile and associated unit tests for these are in the works.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1559 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:49:52 +00:00
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 |
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@/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
91ccb0f8c5
Revert to having these filters use integration over binomial probs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1499 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 01:40:22 +00:00
05c164ec69
changing the default behavior to allow any sized read pile-up (which may exceed the memory limit); the user can then select their own read limit. The default of 100K was arbitrary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1498 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 14:46:00 +00:00
54c0b6c430
Allow this ROD to consist of just the positions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1497 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 12:43:18 +00:00
4a1d79cd7b
added a flag, maximum_reads_at_locus, shortName "mrl", which limits the number of reads we add to the locusByHanger. In some bam files misalignment produces pile-ups of 750K or more reads. We now limit this to the default of 100K reads.
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The user is warned if a locus exceeds this threshold, and no more reads are added.
Also CombineDup walker had an incorrect package name.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1496 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 04:21:58 +00:00
0addae967a
IndelArtifact filter can now handle filtering false SNPs that occur within the span of an indel but after the first position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1495 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 03:34:39 +00:00
85ca68fab6
Initial version: creates a packed file from a fasta, suitable for consumption by BWT-SW. Works with E coli fasta, but will not work at this moment with multi-chr fastas.
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Will be made into a utility routine when BWA comes together.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1494 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 18:39:19 +00:00
591f8eedbb
Added setName() and getName() (however, not used anywhere yet). Now can set the name of the fasta record manually to whatever, however it will work only if done early enough. If the fasta record already started printing itself (i.e. the header line is already done), setName() will throw an exception. Could be too entangled, may reverse this back...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1493 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 18:09:55 +00:00
c9eb193c7f
Now recognizes a special name for a bound rod track: snpmask. If a rod with this name is bound, then ONLY snps from that track will be used (to set alt reference bases to N's), but indels will be ignored. This helps when an alt. ref has to be created for a set of indel calls, and another rod (e.g. dbSNP) is used to put N's in (for sequenom). If dbSNP rod is not marked as "snpmask", the indels reported there will make their way into the alt. reference output and mess it up.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1492 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 18:05:57 +00:00
8e3c3324fa
Added filter for SNPs cleaned out by the realigner.
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It uses the realigner output for filtering; in addition, dbsnp indels partially work; IndelGenotyper calls don't yet work.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1489 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 04:32:32 +00:00
8bc7afe781
Smarter SW penalties
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1488 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 04:29:19 +00:00
463f80c03e
Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1487 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 03:37:24 +00:00
1a299dd459
Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1486 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 03:31:37 +00:00
e70101febc
Add a VEC filter for clustered SNP calls that takes advantage of the new windowed approach; delete the old standalone walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1485 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 03:14:42 +00:00
215e908a11
Reworking of the VariantFiltration system to allow for a windowed view of variants and inclusion of more data to the various filters.
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This now allows us to incorporate both the clustered SNP filter and a SNP-near-indels filter, which otherwise wasn't possible.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1484 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 02:16:39 +00:00
813a4e838f
Removing old code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1482 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 19:27:11 +00:00
49a7babb2c
Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 19:16:30 +00:00
522e4a77ae
Caching support across multiple technologies
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1480 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 18:10:14 +00:00
5af4bb628b
Intermediate checking before code reorganization. Full blown support for empirical transition probs in SSG for all platforms. Support for defaultPlatform arg in SSG. Renaming classes for final cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1479 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 17:34:43 +00:00
6ab9ddf9f5
Significant output formatting improvements. SNPs as indels analysis. heterozygosity rate calculations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1478 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-29 21:49:09 +00:00
bde67428fd
Better formatting of the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1477 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-29 21:46:47 +00:00
8331c195fb
changed the full name of maximum_reads to maximum_iterations for consistancy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1475 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 16:03:46 +00:00
8e129d76fd
Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1474 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 14:14:21 +00:00
f0179109fa
Removing min confidence for on/off genotype
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1473 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 01:04:13 +00:00
4f7ed69242
toString() implemented
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1472 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 01:03:58 +00:00
dc9d40eb9a
Now requires a minimum genotype LOD before applying tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1471 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:19:23 +00:00
37a9b84276
corresponding test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1470 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:17:42 +00:00
bf60980653
Experitmental support for empirical P(B_true | B_miscall). --useEmpiricalTransitions flag to SSG enables this support. Much better implementation of Genotype likelihoods -- the system should scream along now. Continuing progress towards deleting old model
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1469 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:17:24 +00:00
7cf9a54b64
change for new char/byte in BaseUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1467 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-27 23:47:56 +00:00
chartl
ebanks
aaron
depristo
hanna
asivache
kiran
sjia
jmaguire