Because the variable $hadoop_mapping_format is always set to "bam" in HadoopMapping.pm, this indicates that the variable can be clean and the --output-format in the mapper scripts can be removed.
In addition, most of the mappers does not use this variable for anything (all the code is commented) and the ones that still maintain them are gsnap (which overrides and does not use it) and soap (where the output BAM file is probably unused).
We should clean up this argument and the related code to make the scripts simple.
Because the variable
$hadoop_mapping_formatis always set to "bam" inHadoopMapping.pm, this indicates that the variable can be clean and the--output-formatin the mapper scripts can be removed.In addition, most of the mappers does not use this variable for anything (all the code is commented) and the ones that still maintain them are gsnap (which overrides and does not use it) and soap (where the output BAM file is probably unused).
We should clean up this argument and the related code to make the scripts simple.