gatk3的最后一个经典版本3.8

asivache 9652692019 Modified to enable locus traversals firing additional calls to walker's map() with alignment context filled with extended events (indels). Walker should override generateExtendedEvents() to return true, and it should make sure that it catches those additional indel pileups and processes them differently, as needed. If there are indels associated with a specific reference base, TWO map() calls will be issued in locus traversal at that location: first one will have a context filled with a regular base pileup, the second call will provide the context filled with indel pileup (pileup elements will have insertion, deletion, or noevent type associated with them and will also carry information about the full length of the event and inserted bases). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2471 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-29 20:13:25 +00:00
R	Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate.	2009-12-28 20:19:37 +00:00
archive	Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.	2009-12-11 05:28:28 +00:00
c	Add a Unix-standard version number to the file.	2009-11-23 20:07:17 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Modified to enable locus traversals firing additional calls to walker's map() with alignment context filled with extended events (indels). Walker should override generateExtendedEvents() to return true, and it should make sure that it catches those additional indel pileups and processes them differently, as needed. If there are indels associated with a specific reference base, TWO map() calls will be issued in locus traversal at that location: first one will have a context filled with a regular base pileup, the second call will provide the context filled with indel pileup (pileup elements will have insertion, deletion, or noevent type associated with them and will also carry information about the full length of the event and inserted bases).	2009-12-29 20:13:25 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	Adding a package description for making a version of the GATK that only includes the FixBAMSortOrderTag walker.	2009-12-22 00:35:24 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane.	2009-12-28 23:56:49 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag	2009-12-28 22:18:55 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test.	2009-12-28 23:42:46 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00