add samtools fixmate for PE reads about wochenende

[colindaven]

Fixmate needs name sorted, not coord sorted input!

 samtools fixmate
Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>
Options:
  -r           Remove unmapped reads and secondary alignments
  -p           Disable FR proper pair check
  -c           Add template cigar ct tag
  -m           Add mate score tag
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]

As elsewhere in samtools, use '-' as the filename for stdin/stdout. The input
file must be grouped by read name (e.g. sorted by name). Coordinated sorted
input is not accepted.

[colindaven]

Initial implementation

#90