c_cpp/etc/jellyfish/tests/merge.sh

   1 #! /bin/sh
   2
   3 cd tests
   4 . ./compat.sh
   5
   6 sort > ${pref}.md5sum <<EOF
   7 c448e173e5e18264ed00fad0008d5340 ${pref}_quake.histo
   8 EOF
   9 echo "Counting mers and merging" && \
  10     $JF count --quake --matrix seq10m_matrix_19 -m 19 -t $nCPUs \
  11     -o ${pref}_quake -s 3000000 --timing ${pref}_quake.timing seq10m.fq && \
  12     $JF qmerge -s 10000000 -m 19 -o ${pref}_quake_merged ${pref}_quake_[012] && \
  13     $JF qhisto -f -h 3 -i 0.01 -l 0 ${pref}_quake_merged_0 > ${pref}_quake.histo && \
  14     check ${pref}.md5sum
  15 RET=$?
  16
  17 echo "Qmer timing"; cat ${pref}_quake.timing 2>/dev/null
  18 exit $RET