asivache 2fb45dbd73 Make window size a command line argument ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-03 16:13:35 +00:00
..
fasta	Trivial protection for null value	2009-10-27 21:52:52 +00:00
filters	the underlying parameter is a float so we need to use Float.valueOf() instead; Noticed by external user Hou Huabin	2009-11-02 20:22:25 +00:00
genotyper	2nd stage of the genotyper output refactoring is complete.	2009-11-02 22:43:08 +00:00
indels	Make window size a command line argument	2009-11-03 16:13:35 +00:00
recalibration	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
Allows.java	@Required / @Allows flags for main arguments.	2009-05-19 23:26:17 +00:00
By.java	Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along	2009-05-15 21:02:12 +00:00
CountLociWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
CountReadsWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
CountRodByRefWalker.java	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
CountRodWalker.java	Changing the carpet under your feet!! New incremental update to th eROD system has arrived.	2009-09-21 16:55:22 +00:00
DataSource.java	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
DepthOfCoverageWalker.java	bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa	2009-09-09 15:36:12 +00:00
DuplicateWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
LocusWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
LocusWindowWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
PileupWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
PileupWithContextWalker.java	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +00:00
PrintLocusContextWalker.java	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
PrintReadsWalker.java	-Use read.getReadGroup()	2009-10-14 18:08:32 +00:00
RMD.java	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
ReadFilters.java	Better support for specifying read filters to apply directly from the walkers.	2009-07-09 23:59:53 +00:00
ReadWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
RefWalker.java	Added REFERENCE_BASES required annotation for performance	2009-06-18 21:03:57 +00:00
Reference.java	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
Requires.java	@Required / @Allows flags for main arguments.	2009-05-19 23:26:17 +00:00
RodWalker.java	Framework for ROD walkers -- totally experiment and not working right now	2009-09-12 19:13:15 +00:00
SplitSamFileWalker.java	All walkers now use read.getReadGroup()	2009-10-14 19:27:40 +00:00
TreeReducible.java	N-way parallelism. Works for small test cases. Untested for large test cases.	2009-05-01 19:34:09 +00:00
ValidatingPileupWalker.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
Walker.java	bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa	2009-09-09 15:36:12 +00:00
WalkerName.java	Make command-line arguments available in walker constructor, provide back door from	2009-03-26 20:45:27 +00:00
Window.java	Windowed access to the reference.	2009-08-05 16:29:15 +00:00
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00