c_cpp/etc/jellyfish/tests/from_stream.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 EOF
  11
  12 echo "Counting 22-mers on ${nCPUs} CPU" &&      \
  13     cat seq10m.fa | $JF count --matrix seq10m_matrix_22 -m 22 -t $nCPUs -o $pref \
  14     -s 10000000 --timing ${pref}.timing /dev/fd/0 && \
  15     $JF histo -f ${pref}_0 > ${pref}.histo &&      \
  16     echo "GCCATTTCGATTAAAGAATGAT TAGGCATGCAACGCTTCCCTTT" | $JF query ${pref}_0 > ${pref}.query && \
  17     check ${pref}.md5sum
  18 RET=$?
  19
  20 cat ${pref}.timing
  21 # [ -z "$NODEL" ] && \
  22 #     rm -f ${pref}_* ${pref}.histo ${pref}.query ${pref}.md5sum \
  23 #     ${pref}.timing
  24
  25 exit $RET