Queue now does job tracking (replace -run with -status in the command line). Produces output that looks like:
INFO 20:58:17,827 QCommandLine - Checking pipeline status
INFO 20:58:23,234 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_MergeIndels [DONE]
INFO 20:58:23,236 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_158.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,237 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_929.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,238 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_SNP_calls [NOT DONE] 5t/0d/0r/5p/0f
INFO 20:58:23,239 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_HandFilter [NOT DONE]
INFO 20:58:23,240 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_1122.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,240 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_VariantRecalibrator [NOT DONE]
INFO 20:58:23,241 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_913.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,242 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_2037.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,243 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_VariantEval [NOT DONE]
INFO 20:58:23,244 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_Cluster [NOT DONE]
INFO 20:58:23,245 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_106.bam [DONE] 5t/5d/0r/0p/0f
INFO 20:58:23,246 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_Cluster_and_Indel_filter [NOT DONE]
INFO 20:58:23,247 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_ApplyVariantCuts [NOT DONE]
INFO 20:58:23,248 QGraph$$anonfun$formatStatus$1 - Height_Hirschhorn_NHGRI.uncleaned_GenomicAnnotator [NOT DONE]
INFO 20:58:23,248 QGraph$$anonfun$formatStatus$1 - IndelGenotyper_1713.bam [DONE] 5t/5d/0r/0p/0f
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4340 348d0f76-0448-11de-a6fe-93d51630548a
c355afc320