File: do.sh

package info (click to toggle)
genometools 1.6.1%2Bds-3
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 50,412 kB
  • sloc: ansic: 271,241; ruby: 30,339; python: 4,880; sh: 3,193; makefile: 1,194; perl: 219; pascal: 159; haskell: 37; sed: 5
file content (29 lines) | stat: -rwxr-xr-x 521 bytes parent folder | download | duplicates (9)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
#!/bin/sh
checkerror() {
if test $? -ne 0
then
  echo "failure: ${cmd}"
  exit 1
else
  echo "okay: ${cmd}"
fi
}


for cmpcharbychar in 0 1
do
  for dir in fwd rev cpl rcl
  do
    extra=""
    if cmpcharbychar -eq 1
    then
      extra="-cmpcharbychar"
    fi
    cmd="gt suffixerator -dir ${dir} -algbds 3 43 120 -parts 5 -dna -v -pl -bck -tis -suf -lcp -bwt -des -db ${AT} -showtime ${extra}"
    ${cmd}
    checkerror
    cmd="gt dev sfxmap -tis -suf -lcp -bwt -des -esa at1MB"
    ${cmd}
    checkerror
  done
done