c_cpp/etc/jellyfish/tests/from_stream_fastq.sh

   1 #! /bin/sh
   2
   3 cd tests
   4 . ./compat.sh
   5
   6 sort > ${pref}.md5sum <<EOF
   7 c448e173e5e18264ed00fad0008d5340 ${pref}.histo
   8 EOF
   9
  10 echo "Counting 22-mers on ${nCPUs} CPU" &&      \
  11     cat seq10m.fq | $JF count -q --matrix seq10m_matrix_19 -m 19 -t $nCPUs \
  12     -o $pref -s 10000000 --timing ${pref}.timing /dev/fd/0 && \
  13     $JF qhisto -f -h 3 -i 0.01 -l 0.0 ${pref}_0 > ${pref}.histo &&      \
  14     check ${pref}.md5sum
  15 RET=$?
  16
  17 cat ${pref}.timing
  18 # [ -z "$NODEL" ] && \
  19 #     rm -f ${pref}_* ${pref}.histo ${pref}.md5sum ${pref}.timing
  20
  21 exit $RET