4fc1db7aaf
Change interface to VCFWriter add() method to take only 1 byte from reference (since that's the only thing it needs), to prevent bugs like having people call it with ref.addBases() which is wrong (since it provides bases starting from the left of reference context window).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3868 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-23 20:24:03 +00:00
c6ad26e04f
1) When quals/GQs are really integers (x.00), strip off the floating points.
...
2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID. Use a static variable instead.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 18:01:45 +00:00
460283f6d2
No more manually converting VariantContexts to VCFRecords. You should be utilizing VCs and not VCFRecords.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3787 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 05:21:28 +00:00
c9d5345150
Redo StratifiedAlignmentContext to use ReadBackedPileup's stratification options.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3699 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 02:46:05 +00:00
20f5fdbcf7
Changes to MVC to make the the header of its output VCF compliant with spec (give expected # of values for info field annotations)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3660 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 18:33:23 +00:00
75d4736600
Committing changes to comp overlap for indels. Passes all integration tests; minor changes to MVC walker.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3618 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 15:49:13 +00:00
f18ac069e2
A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.
...
Provides a cleaner interface with extended events inheriting all of the basic RBP
functionality. Implementation is still slightly messy, but should allow users to
provide separate implementations of methods for sample split pileups and unsplit
pileups for efficiency's sake.
Methods not covered by unit/integration tests have not been sufficiently tested yet.
Unit tests will follow this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3597 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-20 04:42:26 +00:00
f44d8b150f
Mendelian Violation Classifier now filters violations on the fly via command line arguments; and closes unterminated homozygous regions at the end of a chromosome (so we see arms falling off in the file, rather than in the log)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3592 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 19:32:24 +00:00
20167fd411
Final changes to MVC -- associates variants with regions of homozygosity in child and parents, corrects for genotype errors, and prints out a separate file with informationf or each region of homozygosity.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3521 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:05:37 +00:00
8f9e3e8ad7
Commit for Kiran; but this is now working, barring little exceptions that I've yet to run across...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3511 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 14:21:19 +00:00
736098b58d
A quick commit before running home. This is a re-factored version of the OppositeHomozygoteClassifier which will work with deNovo violations as well. Some code still needs to be migrated from OHC which is wy that walker isn't yet deleted. This'll be up and running tonight.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3502 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 20:47:01 +00:00
delangel
ebanks
hanna
chartl