c_cpp/etc/jellyfish/tests/parallel_fastq_hashing.sh

   1 #! /bin/sh
   2
   3 cd tests
   4 . ./compat.sh
   5
   6 sort > ${pref}.md5sum <<EOF
   7 c448e173e5e18264ed00fad0008d5340 ${pref}.histo
   8 554c9c76fb1f54f2c7526dd1af5aa252 ${pref}_lines.dump
   9 174c7b3873c8aaa5ffee36d5d405bbce ${pref}.stats
  10 EOF
  11 echo "Counting 19-mers qmers, on ${nCPUs} CPU" && \
  12     $JF count --quake --matrix seq10m_matrix_19 -m 19 -t $nCPUs \
  13     -o $pref -s 10000000 --timing ${pref}.timing --stats ${pref}.stats \
  14     seq10m.fq && \
  15     $JF qhisto -f -h 3 -i 0.01 -l 0 ${pref}_0 > ${pref}.histo && \
  16     $JF qdump -c -L 0.035 -U 0.905 ${pref}_0 | wc -l | awk '{ print $1 }' > ${pref}_lines.dump && \
  17     check ${pref}.md5sum
  18 RET=$?
  19
  20 cat ${pref}.timing
  21
  22 exit $RET