convert-sam-for-rsem - Make a RSEM compatible BAM file.

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'.

       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.

       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.

perl v5.38.2                                       2024-04-14                            CONVERT-SAM-FOR-RSEM(1)

       convert-sam-for-rsem - Make a RSEM compatible BAM file.

-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.

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