Fix pipeline bwa_gatk_hg19 for python 3

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2426 bfd2a824-b778-4082-b236-bff916e0c2bb
Try to recover the execution of the pipeline after a race condition has happened.

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2427 bfd2a824-b778-4082-b236-bff916e0c2bb
Minor fixes to the re-winding process

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2428 bfd2a824-b778-4082-b236-bff916e0c2bb
Limit the number of rewinding operations to three to stop ill-designed pipeline to execute indefinitely.

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2429 bfd2a824-b778-4082-b236-bff916e0c2bb
Merge remote-tracking branch 'upstream'