c_cpp/etc/jellyfish/tests/big.sh

   1 #! /bin/sh
   2
   3 cd tests
   4 . ./compat.sh
   5
   6 if [ -z "$BIG" ]; then
   7     echo "Skip big test"
   8     exit 77
   9 fi
  10
  11 sort > ${pref}.md5sum <<EOF
  12 f52abd3e2a7cc5089cc8f32cb607c4c5 ${pref}_16.histo
  13 eac5dafa9db7af2c5202dec8c6c33d00 ${pref}_16.stats
  14 EOF
  15
  16     # $JF count -m 31 -s 4000000000 -o ${pref}_31 -c 4 -p 253 -C -r -t $nCPUs --timing ${pref}_31.timing \
  17     # seq30g.fa && \
  18     # $JF histo ${pref}_31_0 > ${pref}_31.histo && \
  19
  20 echo "Generate 30 Gigs of sequence and count k-mers on it" && \
  21     ([ -f seq30g.fa ] || ${DIR}/generate_sequence -v -o seq30g -r 1000 -s 1602176487 30000000000) && \
  22     $JF count -m 16 -s 4000000000 -o ${pref}_16 -c 4 -p 253 -C --out-counter-len 2 \
  23     -t $nCPUs --timing ${pref}_16.timing --stats ${pref}_16.stats $JFPARAM seq30g.fa && \
  24     $JF histo ${pref}_16_0 > ${pref}_16.histo && \
  25     check ${pref}.md5sum
  26 RET=$?
  27
  28 echo "16-mer timing"; cat ${pref}_16.timing
  29
  30 exit $RET