abra 2.12 lazy patch (#74)

* rewrite parser for 1.129 and mark dups

* increment default version, expose all cmo versions

* move picard object into cmo_picard to reduce installation/testing time

* 1.7.0 version increment

* /bin/bash

* remove __init__.py picard reference so installation works

* fix dumb print statements

* don't pass version arg to sing.sh

* use platform unit to label chunked fastqs

* switch to platforum unit to label fastqs is breaking, increment minor version

* return 0 in failure

* 1.8.1 version increment

* sync this up with cluster

* commit singularity debug log for bcftools

* update cmoqcpdf for roslin-qc 0.5.8- cumbersomely technical debt here, but leave it while we decide on refactor

* update version

* auto log LSB_JOBID if present

* default thresholds for coverage should be 50/25

* int/float for qcpdf variables

* update version

bin/cmo_abra

@@ -120,8 +120,10 @@ def convert_default_variables(parser):
             del args.working
             del args.bwa_ref
     except:#default version
-        del args.working
-        del args.bwa_ref
+        if 'working' in args:
+            del args.working
+        if 'bwa_ref' in args: 
+            del args.bwa_ref
 
     if not args.targets:
         args.targets = cmo.util.targets['abra'][args.ref]

bin/cmo_qcpdf

@@ -47,7 +47,6 @@ if __name__ == "__main__":
     parser.add_argument("--duplication-threshold", type=int, default="50")
     parser.add_argument("--cov-warn-threshold", type=int, default="50")
     parser.add_argument("--cov-fail-threshold", type=int, default="25")
-
     parser.add_argument("--version", default="0.5.8", choices=cmo.util.programs['roslin-qc'].keys())
     args = parser.parse_args()
 #    script = os.path.join(cmo.util.programs['roslin-qc'][args.version], "generate_pdf.py")

cmo/_version.py

@@ -4,5 +4,5 @@
 
 
 
-__version__ = '1.9.2'
+__version__ = '1.9.3'