NAME

       convert-sam-for-rsem

PURPOSE

       Make a RSEM compatible BAM file.

SYNOPSIS

        convert-sam-for-rsem [options] <input.sam/input.bam/input.cram> output_file_name

ARGUMENTS

       input.sam/input.bam/input.cram
           The SAM/BAM/CRAM file generated by user's aligner. We require this file contains the
           header section.

       output_file_name
           The output name for the converted file. 'convert-sam-for-rsem' will output a BAM with
           the name 'output_file_name.bam'.

OPTIONS

       -p/--num-threads <int>
           Set the number of threads to be used for converting. (Default: 1)

       --memory-per-thread <string>
           Set the maximum allowable memory per thread. <string> represents the memory and
           accepts suffices 'K/M/G'. (Default: 1G)

       -h/--help
           Show help information.

DESCRIPTION

       This program converts the SAM/BAM/CRAM file generated by user's aligner into a BAM file
       which RSEM can process. However, users should make sure their aligners use
       'reference_name.idx.fa' generated by 'rsem-prepare-reference' as their references and
       output header sections. After the conversion, this program will call 'rsem-sam-validator'
       to validate the resulting BAM file.

       Note: You do not need to run this script if `rsem-sam-validator' reports that your
       SAM/BAM/CRAM file is valid.

EXAMPLES

       Suppose input is set to 'input.sam' and output file name is "output"

        convert-sam-for-rsem input.sam output

       We will get a file called 'output.bam' as output.