14 Commits (5cc1e72fdbb179a54d295f835b52bf11399edc59)

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
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	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	19e27d4568	Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.	2011-10-27 23:55:11 -04:00
Eric Banks	4a7e6fee3f	Remove support for BED file interval parsing in the GATK; it should all go through Tribble now. IndelRealigner no longer supports unordered interval input (which shouldn't have been used anyways). Temporarily commenting out serialization of arguments so that tests pass; this whole piece will be deleted soon anyways.	2011-10-27 13:38:08 -04:00
Eric Banks	68283b1651	Fixing docs and adding GATKdocs for the new interval functionality	2011-10-26 22:14:43 -04:00
Eric Banks	9424e8b2ca	Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed.	2011-10-26 14:11:49 -04:00
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
Mark DePristo	f3049fba63	refdata directory cleanup ... Removing unused files RODRecordIterator, ReferenceOrderedData, QueryableTrack, RMDTrackCreationException, GATKFeatureIterator, ReferenceOrderedDataUnitTest Refactored dbSNP and refseq utilities to be closer to the other files implementing these features	2011-07-25 13:21:52 -04:00
Mark DePristo	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
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