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add -z to disable markdup in align #121

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add -z to disable markdup in align #121

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696e035
add -z to disable markdup in align
lozybean Dec 14, 2017
e68bbc9
add -z usage
lozybean Dec 14, 2017
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15 changes: 10 additions & 5 deletions bin/speedseq
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Original file line number Diff line number Diff line change
Expand Up @@ -212,6 +212,7 @@ alignment options:

samblaster options:
-i include duplicates in splitters and discordants
-z do not mark duplicate
-c INT maximum number of split alignments for a read to be included in splitter file [2]
-m INT minimum non-overlapping base pairs between two alignments for a read to be included in splitter file [20]

Expand Down Expand Up @@ -239,6 +240,7 @@ global options:
RG_FMT=""
OUTPUT=""
INCLUDE_DUPS="--excludeDups"
MARK_DUPS=""
MAX_SPLIT_COUNT=2
MIN_NON_OVERLAP=20
THREADS=1
Expand All @@ -247,7 +249,7 @@ global options:
INS_DIST=""
SORT_MEM=20 # amount of memory for sorting, in gigabytes

while getopts ":hw:o:R:pic:m:M:t:T:I:vK:" OPTION
while getopts ":hw:o:R:pizc:m:M:t:T:I:vK:" OPTION
do
case "${OPTION}" in
h)
Expand All @@ -270,6 +272,9 @@ global options:
c)
MAX_SPLIT_COUNT="$OPTARG"
;;
z)
MARK_DUPS="--acceptDupMarks"
;;
m)
MIN_NON_OVERLAP="$OPTARG"
;;
Expand Down Expand Up @@ -422,7 +427,7 @@ global options:
then
echo -e "
$BWA mem -t $THREADS -p $INS_DIST $RG_FMT $REF $FQ | \\
$SAMBLASTER $INCLUDE_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \\
$SAMBLASTER $INCLUDE_DUPS $MARK_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \\
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \\
$SAMBAMBA sort -t $THREADS -m $((${SORT_MEM}-2))G --tmpdir=$TEMP_DIR/full -o $OUTPUT.bam /dev/stdin

Expand All @@ -436,7 +441,7 @@ global options:

echo "
$BWA mem -t $THREADS -p $INS_DIST $RG_FMT $REF $FQ | \
$SAMBLASTER $INCLUDE_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \
$SAMBLASTER $INCLUDE_DUPS $MARK_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \
$SAMBAMBA sort -t $THREADS -m $((${SORT_MEM}-2))G --tmpdir=$TEMP_DIR/full -o $OUTPUT.bam /dev/stdin

Expand All @@ -452,7 +457,7 @@ global options:
then
echo -e "
$BWA mem -t $THREADS $INS_DIST $RG_FMT $REF $FQ1 $FQ2 | \\
$SAMBLASTER $INCLUDE_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \\
$SAMBLASTER $INCLUDE_DUPS $MARK_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \\
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \\
$SAMBAMBA sort -t $THREADS -m $((${SORT_MEM}-2))G --tmpdir=$TEMP_DIR/full -o $OUTPUT.bam /dev/stdin

Expand All @@ -466,7 +471,7 @@ global options:

echo "
$BWA mem -t $THREADS $INS_DIST $RG_FMT $REF $FQ1 $FQ2 | \
$SAMBLASTER $INCLUDE_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \
$SAMBLASTER $INCLUDE_DUPS $MARK_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP --splitterFile $TEMP_DIR/spl_pipe --discordantFile $TEMP_DIR/disc_pipe | \
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \
$SAMBAMBA sort -t $THREADS -m $((${SORT_MEM}-2))G --tmpdir=$TEMP_DIR/full -o $OUTPUT.bam /dev/stdin

Expand Down