Prevent index from failing when index already exists

Update _version.py

Increased version

Merge branch 'master' of https://github.com/mskcc/cmo

Increase chunk size in split_reads; support GRCh37_mm10 in vcf2maf

Deduplicate BAMs with the same sample IDs

Update _version.py

Merge pull request #77 from mskcc/new_picard

New Picard and qc fix

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

Delly cmo wrapper (#71)

* on local

* Added delly

* Fixed delly handling of version

* More modifications:
- fixed bugs
- automatically pull the exclusion file based on genome
- give the user the option to specify a file/use all regions

* Increment version

* Fixed a simple bug in delly command generation

* Removed artifact file