fix a duplicate line in vcf.fmt

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2515 bfd2a824-b778-4082-b236-bff916e0c2bb
Fix a counting bug with Python 3

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2516 bfd2a824-b778-4082-b236-bff916e0c2bb
Open the 2.3.0 development cycle

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2517 bfd2a824-b778-4082-b236-bff916e0c2bb
Fixing DecompressFiles pipeline functor when there are directory structure inside the tar file

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2518 bfd2a824-b778-4082-b236-bff916e0c2bb
Add pipeline bwa_gatk28_hg19 (the resource bundle of gatk 2.3 is no longer available)

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2519 bfd2a824-b778-4082-b236-bff916e0c2bb
Sort pipelines for the output vtools show pipelines

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2520 bfd2a824-b778-4082-b236-bff916e0c2bb
Raise an error when a resource file fails to download

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2521 bfd2a824-b778-4082-b236-bff916e0c2bb
Python3 compatibility fixes

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2522 bfd2a824-b778-4082-b236-bff916e0c2bb
Python 3 compatibility

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2523 bfd2a824-b778-4082-b236-bff916e0c2bb
Accept compressed fastq files in tar files in the bwa_gatk_hg19 pipeline. Use read names to pair filenames before using filenames. This is a more accurate method to pair files

git-svn-id: https://svn.code.sf.net/p/varianttools/code/trunk@2524 bfd2a824-b778-4082-b236-bff916e0c2bb
Merge remote-tracking branch 'upstream'