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17 Commits (7204fcc2c353315f4c990a91761ba0a6afabdbf9)

Author SHA1 Message Date
David Roazen 1296dd41be Removing the legacy -L "interval1;interval2" syntax 
This syntax predates the ability to have multiple -L arguments, is
inconsistent with the syntax of all other GATK arguments, requires
quoting to avoid interpretation by the shell, and was causing
problems in Queue.

A UserException is now thrown if someone tries to use this syntax.
 2011-11-21 13:18:53 -05:00
Khalid Shakir c50274e02e During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. 
Moved flanking interval utilies to IntervalUtils with UnitTests.
 2011-11-17 13:56:42 -05:00
Eric Banks 02d5e3025e Added integration test for intervals from bed file 2011-11-09 15:34:19 -05:00
Mark DePristo 392e0aeace Moved unit tests into master IntervalUtilsUnitTest 2011-11-02 10:52:00 -04:00
Mark DePristo c2b97030a4 IntervalUtils for completely balanced locus-based scatter/gather 
-- scatterLocusIntervals master utility
-- Moved around some general functionality from GenomeLocSortedSet to GenomeLoc
-- Util function for reversing a list (List<T> -> List<T>, unlike Collections version)
-- DoC is PartitionType.INTERVAL
-- Significant unit tests on new functionality (all passing)
-- Ready for real-world testing, as soon as I can get LocusScatterFunction.scala to actually work
 2011-11-02 10:49:40 -04:00
Eric Banks 0ca7428e76 Allow processing of empty intervals, but warn user when this case is encountered. 2011-10-28 12:12:14 -04:00
Eric Banks 8b1a62da27 Adding unit test to cover overlapping intervals from the same source with the intersection rule. 2011-10-28 09:59:43 -04:00
Eric Banks 6ba08a103d Empty ROD files should generate an exception when used for creating intervals. Moved some now obsolete files to the archive as the realigner will now read all target intervals into memory. 2011-10-28 09:23:25 -04:00
Eric Banks ccfd853b34 Added further integration tests for rod-based intervals that deal with more complex cases. Good call by Mark to test the empty VCF example because we were failing on it; fixed. 2011-10-27 20:43:50 -04:00
Eric Banks 8c4dbce6d8 Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing. 2011-10-27 13:58:19 -04:00
Eric Banks 3273c20c98 Added integration tests for Tribble-based intervals and fixed up some of the other tests based on some method changes. 2011-10-26 15:29:18 -04:00
Mark DePristo 9bd3ba4c7e Missed one MD5 2011-10-04 16:04:52 -07:00
Mark DePristo ffdfdcde3f Updating MD5s 
-- Interval test now uses RG containing BAM
-- DoC sample name ordering has changed.
 2011-10-04 15:54:45 -07:00
Mark DePristo 4ad330008d Final intervals cleanup 
-- No functional changes (my algorithm wouldn't work)
-- Major structural cleanup (returning more basic data structures that allow us to development new algorithm)
-- Unit tests for the efficiency of interval partitioning
 2011-09-19 10:19:10 -04:00
Mark DePristo 72536e5d6d Done 2011-09-09 15:44:47 -04:00
Mark DePristo 06cb20f2a5 Intermediate commit cleaning up scatter intervals 
-- Adding unit tests to ensure uniformity of intervals
 2011-09-09 12:56:45 -04:00
David Roazen 3c9497788e Reorganized the codebase beneath top-level public and private directories, 
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
 2011-06-28 06:55:19 -04:00