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BamLeftAlign tool help

BamLeftAlign (0.1-420-g3536bb0)

Iteratively left-aligns and merges the insertions and deletions in all alignments.

Mandatory parameters:
  -in <file>      Input BAM file.
  -out <file>     Output BAM file.

Optional parameters:
  -ref <file>     Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                  Default value: ''
  -max_iter <int> Maximum number of iterations per read.
                  Default value: '50'
  -v              Verbose mode: Prints changed/unstable alignment names to the command line.
                  Default value: 'false'

Special parameters:
  --help          Shows this help and exits.
  --version       Prints version and exits.
  --changelog     Prints changeloge and exits.
  --tdx           Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.

BamLeftAlign changelog

BamLeftAlign 0.1-420-g3536bb0

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