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Disabling pipefail when the output is explicitely troncated #230

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Disabling pipefail when the output is explicitely troncated #230

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8 changes: 8 additions & 0 deletions scripts/lumpyexpress
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Original file line number Diff line number Diff line change
Expand Up @@ -401,15 +401,19 @@ then

# generate discordant pair string for LUMPY
DISC_BAM=$TEMP_DIR/$OUTBASE.sample$(($i+1)).discordants.bam
set +o pipefail
DISC_SAMPLE=`$SAMT view $EXT_OPT -H $FULL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
set -o pipefail
RG_STRING=`echo "${LIB_RG_LIST[$j]}" | sed 's/,/,read_group:/g' | sed 's/^/read_group:/g'`
MEAN=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^mean" | sed 's/mean\://g'`
STDEV=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^stdev" | sed 's/stdev\://g'`
LUMPY_DISC_STRING="$LUMPY_DISC_STRING -pe bam_file:${DISC_BAM},histo_file:${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).x4.histo,mean:${MEAN},stdev:${STDEV},read_length:${READ_LENGTH},min_non_overlap:${READ_LENGTH},discordant_z:5,back_distance:10,weight:1,id:${DISC_SAMPLE},min_mapping_threshold:20,${RG_STRING}"

# generate split-read string for LUMPY
SPL_BAM=$TEMP_DIR/$OUTBASE.sample$(($i+1)).splitters.bam
set +o pipefail
SPL_SAMPLE=`$SAMT view $EXT_OPT -H $FULL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
set -o pipefail
LUMPY_SPL_STRING="$LUMPY_SPL_STRING -sr bam_file:${SPL_BAM},back_distance:10,min_mapping_threshold:20,weight:1,id:${SPL_SAMPLE},min_clip:20,${RG_STRING}"
done

Expand Down Expand Up @@ -487,15 +491,19 @@ else
echo "done"

# construct LUMPY_SPL_STRING
set +o pipefail
SPL_SAMPLE=`$SAMT view -H $SPL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
set -o pipefail
LUMPY_SPL_STRING="$LUMPY_SPL_STRING -sr bam_file:${SPL_BAM},back_distance:10,min_mapping_threshold:20,weight:1,id:${SPL_SAMPLE},min_clip:20"

# construct LUMPY_DISC_STRING
for j in $( seq 0 $(( ${#LIB_RG_LIST[@]}-1 )) )
do
echo $(( ${#FULL_BAM_LIST[@]}-1 ))
DISC_BAM=${DISC_BAM_LIST[$i]}
set +o pipefail
DISC_SAMPLE=`$SAMT view -H $DISC_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
set -o pipefail
MEAN=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^mean" | sed 's/mean\://g'`
STDEV=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^stdev" | sed 's/stdev\://g'`
RG_STRING=`echo "${LIB_RG_LIST[$j]}" | sed 's/,/,read_group:/g' | sed 's/^/read_group:/g'`
Expand Down