gatk3的最后一个经典版本3.8

delangel f64b6fddc1 Major changes/improvements to indel genotyper: ... a) Redid way to compute path metrics in indel error model. Paper formulation where we have an anchor point in the alignemt between read and haplotype won't work in practice except in nice data sets that are perfectly indel-realigned and that are well mapped by aligner. New formulation doesn't assume this, and it's actually simpler and uses less code. It now resembles more a classic SW dynamic programming formulation but it still preserves the HMM probabilistic formulation. b) Added a programmable call threshold, set by command line. c) Use now sample name from BAM file, remove -sampleName argument. d) Simplify loop to compute read-haplotype likelihoods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4311 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-19 23:47:31 +00:00
R	improvements to the report code	2010-09-15 00:45:13 +00:00
archive	Cleaning up playground utils and tests	2010-08-27 01:25:47 +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	Major changes/improvements to indel genotyper:	2010-09-19 23:47:31 +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	Fix for DoC issue with multiplexer -- will retire use of multiplexer when	2010-09-07 00:44:07 +00:00
perl	- Update DoC to support output to /dev/null.	2010-09-08 23:43:18 +00:00
python	Do this the right way	2010-09-19 04:30:48 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Told people this worked...forgot to commit!	2010-09-18 03:46:00 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	Fixed header generation when lines contain spaces.	2010-09-17 17:14:59 +00:00
testdata	and add changes to the vcf used in testing	2010-06-25 02:56:02 +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	- Include the fasta index builder in the package.	2010-09-08 20:37:54 +00:00
ivy.xml	Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis	2010-09-15 11:50:22 +00:00