gatk-3.8/shell/calcCallerMD5s.csh

#!/bin/tcsh

foreach model (ONE_STATE THREE_STATE EMPIRICAL)
java -Xmx4096m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -L 1:10,000,000-11,000,000 -R /broad/1KG/reference/human_b36_both.fasta -T SingleSampleGenotyper -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout ./$model.geli.calls -lod 5 -m $model
end
wc -l *.geli.calls
md5sum *.geli.calls
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! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a 2009-09-04 20:39:06 +08:00			`#!/bin/tcsh`

			`foreach model (ONE_STATE THREE_STATE EMPIRICAL)`
			`java -Xmx4096m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -l INFO -L 1:10,000,000-11,000,000 -R /broad/1KG/reference/human_b36_both.fasta -T SingleSampleGenotyper -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout ./$model.geli.calls -lod 5 -m $model`
			`end`
			`wc -l *.geli.calls`
			`md5sum *.geli.calls`