BamLeftAlign (0.1-222-g9be2128)
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 0.1-222-g9be2128