a8d08ea18d
As a user pointed out, it is not valid for a GenomeLoc to have a start or stop equal to 0.
2012-07-17 22:18:43 -04:00
62cee2fb5b
Feature request from Tim that could be useful to all: there's now an --interval_padding argument that specifies how many basepairs to add to each of the intervals provided with -L (on both ends). This is particularly useful when trying to run over the exome plus flanks and don't want to have to pre-compute the flanks (just use e.g. --interval_padding 50). Added integration test to cover this feature.
2012-06-18 21:36:27 -04:00
40431890be
-- BCF2 is now a reference dependent codec so it can initialize the contigs in the case where the file doesn't have contigs in it
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-- BCF2 writer can now work without the contig lines being in the header
-- Made GenomeLocParser a final class
2012-05-24 10:57:06 -04:00
252e0f3d0a
Merged bug fix from Stable into Unstable
2011-12-08 13:11:39 -05:00
1bfe28067f
Don't try to genotype an indel even bigger than the reference window size, or else we'll be out of bounds. Necessary to handle Phase 1 integrated callset with large deletions. Better error indication when validating a GenomeLoc.
2011-12-08 12:54:08 -05:00
022832bd74
Very bad use of the == operator with Strings was ensuring that validating GenomeLocs was very inefficient. This fix resulted in a significant speedup for a simple RodWalker.
2011-11-21 14:49:47 -05:00
c50274e02e
During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
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Moved flanking interval utilies to IntervalUtils with UnitTests.
2011-11-17 13:56:42 -05:00
dc4932f93d
VariantEval module to stratify the variants by whether they overlap an interval set
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The primary use of this stratification is to provide a mechanism to divide asssessment of a call set up by whether a variant overlaps an interval or not. I use this to differentiate between variants occurring in CCDS exons vs. those in non-coding regions, in the 1000G call set, using a command line that looks like:
-T VariantEval -R human_g1k_v37.fasta -eval 1000G.vcf -stratIntervals:BED ccds.bed -ST IntervalStratification
Note that the overlap algorithm properly handles symbolic alleles with an INFO field END value. In order to safely use this module you should provide entire contigs worth of variants, and let the interval strat decide overlap, as opposed to using -L which will not properly work with symbolic variants.
Minor improvements to create() interval in GenomeLocParser.
2011-11-10 10:58:40 -05:00
800bb97f0b
Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser
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Updated all walkers that used the now deleted methods.
2011-08-03 16:04:51 -04:00
9992c373be
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
2011-07-17 20:29:58 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Eric Banks
Mark DePristo
Guillermo del Angel
Khalid Shakir
David Roazen