gatk3的最后一个经典版本3.8

asivache aadd230636 N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir). ... Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent (it has been already taking ;-separated args in unsorted mode) NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4602 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-01 16:06:51 +00:00
R	Takes a list of BAMs, looks up the read group information in the sequencing platform's SQUID database, and computes the tearsheet stats. Also takes the VariantEval output (R format) and outputs the variant stats and some plots for the tearsheet. This script requires the gsalib library to be in the R library path (add the line '.libPaths('/path/to/Sting/R/')' to your ~/.Rprofile).	2010-10-27 19:06:22 +00:00
archive	Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.	2010-10-22 20:35:53 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir).	2010-11-01 16:06:51 +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	Include all standard annotations	2010-10-11 20:52:08 +00:00
perl	Also removed contig intervals from the pipeline sanity check perl scsript.	2010-10-21 11:23:34 +00:00
python	Commenting out annoying print statement	2010-10-24 11:55:26 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Now that the user is required to set the java temp directory, it is safer for the LsfJobRunner to write to the java temp directory instead of the command directory.	2010-10-28 15:00:21 +00:00
settings	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00
shell	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +00:00
testdata	Fixes for example bam files	2010-10-05 18:43:02 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Cleanup for multithreading memory leak during integration tests...unregister MXBean at end	2010-10-28 18:37:42 +00:00
ivy.xml	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00