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Window size flag and testing #2

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Merged
s-boardman merged 1 commit into from
Sep 21, 2015
Merged

Window size flag and testing #2

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16 changes: 14 additions & 2 deletions bin/speedseq
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Original file line number Diff line number Diff line change
Expand Up @@ -1157,6 +1157,7 @@ sv options:
-x FILE BED file to exclude
-g genotype SV breakends with svtyper
-d calculate read-depth with CNVnator
-w CNVnator window size [100]
-A annotate the vcf with VEP
-P output LUMPY probability curves in VCF
-m INT minimum sample weight for a call [4]
Expand Down Expand Up @@ -1188,8 +1189,9 @@ global options:
OUTPUT=""
MAX_SPLIT_COUNT=2
MIN_NON_OVERLAP=20
WIN_SIZE=100

while getopts ":hB:S:D:R:o:m:r:x:T:t:AdgPkvK:" OPTION
while getopts ":hB:S:D:R:o:m:r:x:T:t:AdwgPkvK:" OPTION
do
case "${OPTION}" in
h)
Expand Down Expand Up @@ -1235,6 +1237,9 @@ global options:
d)
READDEPTH=1
;;
w)
WINDOW_SIZE="$OPTARG"
;;
g)
GENOTYPE=1
;;
Expand Down Expand Up @@ -1344,6 +1349,14 @@ global options:
exit 1
fi
fi

# if window size specified, check CNVnator is also specified
if [[ "$WINDOW_SIZE" -eq 100 ]] && [[ "$READDEPTH" ! -eq 1 ]]
then
sv_usage
echo -e "CNVnator window size passed without CNVnator; please use -d in conjunction with -w"
exit 1
fi

# check for required python modules (pysam, numpy, scipy, etc)
check_python_modules $PYTHON
Expand Down Expand Up @@ -1439,7 +1452,6 @@ global options:
if [[ "$READDEPTH" -eq 1 ]]
then
echo "Calculating read depth"
WINDOW_SIZE=100

for i in $( seq 0 $(( ${#FULL_BAM_LIST[@]}-1 )) )
do
Expand Down