c_cpp/etc/jellyfish/tests/min_qual.sh

   1 #! /bin/sh
   2
   3 cd tests
   4 . ./compat.sh
   5
   6 sort > ${pref}.md5sum <<EOF
   7 7f78bc16dedc972fc253bf1378e01561 ${pref}.histo
   8 EOF
   9
  10 echo "Counting 22-mers on ${nCPUS} CPU" && \
  11     $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o $pref \
  12     -s 10000000 --timing ${pref}.timing --min-quality 3 seq10m.fq && \
  13     $JF histo -f ${pref}_0 > ${pref}.histo && \
  14     check ${pref}.md5sum
  15 RET=$?
  16
  17 cat ${pref}.timing 2>/dev/null
  18 exit $RET