c_cpp/etc/jellyfish/tests/parallel_hashing.sh

   1 #! /bin/sh
   2
   3 cd tests
   4 . ./compat.sh
   5
   6 sort > ${pref}.md5sum <<EOF
   7 4fd24c05f7c18c47e7b69f77aa071f1f ${pref}_0
   8 7059a4e90b6670b2d814e44e2bc7d429 ${pref}.histo
   9 c3233e107bb6b42d0c979707f156264c ${pref}.query
  10 dbe881e4649406321d0e481da08eab5c ${pref}_L.dump
  11 dbe881e4649406321d0e481da08eab5c ${pref}.dump
  12 a210906960cf36c09eecad62a4c04973 ${pref}.stats
  13 EOF
  14 echo "Counting 22-mers on ${nCPUs} CPU" &&      \
  15     $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o $pref \
  16     -s 10000000 --timing ${pref}.timing --stats ${pref}.stats seq10m.fa && \
  17     $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o ${pref}_L \
  18     -s 10000000 --timing ${pref}.timing -L 2 seq10m.fa && \
  19     $JF histo -f ${pref}_0 > ${pref}.histo &&      \
  20     $JF dump -c ${pref}_L_0 > ${pref}_L.dump && \
  21     $JF dump -c -L 2 ${pref}_0 > ${pref}.dump && \
  22     echo "GCCATTTCGATTAAAGAATGAT TAGGCATGCAACGCTTCCCTTT" | $JF query ${pref}_0 > ${pref}.query && \
  23     check ${pref}.md5sum
  24 RET=$?
  25
  26 cat ${pref}.timing
  27
  28 exit $RET