Commit ece0afa1 authored by Robin Erich Muench's avatar Robin Erich Muench
Browse files

update metaSNP_COV -P fix

parent a580e728
......@@ -29,7 +29,7 @@ display_usage() {
echo >&2 " all_samples FILE Input list of bam files, one file per line."
echo >&2 ""
echo >&2 " Options:"
echo >&2 " -P Print a commandline job for each sample in all_samples"
echo >&2 " -P Print a commandline job for each sample in all_samples"
echo >&2 ""
}
......@@ -41,22 +41,22 @@ missing() {
echo >&2 ""
echo >&2 "ERROR: '$1' no such file or directory"
display_usage
exit 1
exit
}
make_dir() {
echo >&2 ""
echo >&2 "ERROR: '$1' is not a metaSNP project. Subdirectory '$2' is missing."
echo >&2 ""
echo >&2 ""
echo >&2 "Please initialize a new metaSNP project first!"
echo >&2 ""
echo >&2 " RUN: metaSNP_NEW projectName"
echo >&2 "or"
echo >&2 " RUN: mkdir $2"
echo >&2 ""
echo >&2 ""
echo >&2 " RUN: metaSNP_NEW projectName"
echo >&2 "or"
echo >&2 " RUN: mkdir $2"
echo >&2 ""
# display_usage
# mkdir $OUT_DIR
exit 1
exit
}
......@@ -123,12 +123,12 @@ done<$all_samples
## Generate command lines
while read file
do
if [ $PRINT ]
name=$(basename $file)
cmdline="$DIR/src/qaTools/qaCompute -c 10 -d -i $file $OUT_DIR/$name.cov"
if [ $PRINT ] ;
then
name=$(basename $file)
echo $DIR/src/qaTools/qaCompute -c 10 -d -i $file $OUT_DIR/$name.cov
echo $cmdline
else
$DIR/src/qaTools/qaCompute -c 10 -d -i $file $OUT_DIR/$name.cov
eval $cmdline
fi
done < $all_samples
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