aaron db9570ae29 Looks bigger than it is: ... * Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes). * Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify: "-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-15 00:14:35 +00:00
..
arguments	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
contexts	-UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one)	2010-01-08 05:40:42 +00:00
datasources	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
examples	Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.	2009-12-13 04:13:30 +00:00
executive	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00
filters	Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark.	2010-01-03 21:31:04 +00:00
io	Additional sanity checking: make sure the user can't alter the header / compression level / presorted state of a file to which SAMRecords have already been written.	2010-01-12 18:39:41 +00:00
iterators	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
refdata	added: peekNextLocation(); it's quite hard (and probably unnecessary, ever) to make seekable iterator a peekable one, but it is quite easy and useful to be able to peek just the next location the iterator will jump to after next call to next()	2010-01-14 17:38:19 +00:00
traversals	Make sure that reference view holds enough bases to pass full-length deleted sequence to the walker's map() function in extended event mode (this addresses the problem of a deletion crossing the shard's boundary, so that an attempt to extract deleted bases results in a crash)	2010-01-07 22:37:22 +00:00
walkers	PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests.	2010-01-13 20:09:10 +00:00
CommandLineExecutable.java	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
CommandLineGATK.java	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
GenomeAnalysisEngine.java	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
Reads.java	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
WalkerManager.java	Cleanup of the doc system, and introduce Kiran's concept of a detailed summary	2009-12-12 04:04:37 +00:00
package-info.java	Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file	2009-12-04 20:08:41 +00:00