issue 122: preliminary fix to getline issue
upgraded to samtools 0.1.19
issue 107 - pileup(truncate) now works
issue 114 - fixed order in cigarstring
issue 116 - accept filename.bai indices.
issue 129 - memory issue with python/char* conversion
issue 113 - better error message for malformatted header
issue 115 - long tags added test case
Merge remote-tracking branch upstream/$:{upbranch}