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Improve align() by using process substitution (replace named pipe) #48

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Improve align() by using process substitution (replace named pipe) #48

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90 changes: 35 additions & 55 deletions bin/speedseq
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Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ global options:
;;
R)
RG="$OPTARG"
RG_FMT="-R '$OPTARG'"
RG_FMT="-R $OPTARG"
;;
p)
INTERLEAVED=1
Expand Down Expand Up @@ -353,21 +353,11 @@ global options:

if [[ $VERBOSE -eq 1 ]]
then
echo "
mkdir -p $TEMP_DIR/full $TEMP_DIR/spl $TEMP_DIR/disc
mkfifo $TEMP_DIR/spl_pipe $TEMP_DIR/disc_pipe"
echo "mkdir -p $TEMP_DIR/full $TEMP_DIR/spl $TEMP_DIR/disc"
fi

# create temp files
mkdir -p $TEMP_DIR/full $TEMP_DIR/spl $TEMP_DIR/disc
if [[ ! -e $TEMP_DIR/spl_pipe ]]
then
mkfifo $TEMP_DIR/spl_pipe
fi
if [[ ! -e $TEMP_DIR/disc_pipe ]]
then
mkfifo $TEMP_DIR/disc_pipe
fi

# alignment command
if [[ "$INTERLEAVED" -eq 1 ]]
Expand All @@ -376,63 +366,53 @@ 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 --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP \\
--splitterFile >(gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" | \\
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin) \\
--discordantFile >(gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" | \\
$SAMBAMBA view -S -f bam /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin) | \\
$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

gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/spl_pipe | \\
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin
gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/disc_pipe | \\
$SAMBAMBA view -S -f bam /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin"
$SAMBAMBA sort -t $THREADS -m $((${SORT_MEM}-2))G --tmpdir=$TEMP_DIR/full -o $OUTPUT.bam /dev/stdin"
fi

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 | \
$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

gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/spl_pipe | \
$BWA mem -t $THREADS -p $INS_DIST $RG_FMT $REF $FQ | \
$SAMBLASTER $INCLUDE_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP \
--splitterFile >(gawk '{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }' OFS="\t" | \
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin
gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/disc_pipe | \
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin) \
--discordantFile >(gawk '{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }' OFS="\t" | \
$SAMBAMBA view -S -f bam /dev/stdin | \
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin
" | $PARALLEL -j 3
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin) | \
$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
else
if [[ $VERBOSE -eq 1 ]]
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 --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP \\
--splitterFile >(gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" | \\
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin) \\
--discordantFile >(gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" | \\
$SAMBAMBA view -S -f bam /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin) | \\
$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

gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/spl_pipe | \\
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin
gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/disc_pipe | \\
$SAMBAMBA view -S -f bam /dev/stdin | \\
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin"
$SAMBAMBA sort -t $THREADS -m $((${SORT_MEM}-2))G --tmpdir=$TEMP_DIR/full -o $OUTPUT.bam /dev/stdin"
fi

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 | \
$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

gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/spl_pipe | \
$BWA mem -t $THREADS $INS_DIST $RG_FMT $REF $FQ1 $FQ2 | \
$SAMBLASTER $INCLUDE_DUPS --addMateTags --maxSplitCount $MAX_SPLIT_COUNT --minNonOverlap $MIN_NON_OVERLAP \
--splitterFile >(gawk '{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }' OFS="\t" | \
$SAMBAMBA view -S -f bam -l 0 /dev/stdin | \
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin
gawk '{ if (\$0~\"^@\") { print; next } else { \$10=\"*\"; \$11=\"*\"; print } }' OFS=\"\\t\" $TEMP_DIR/disc_pipe | \
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/spl -o $OUTPUT.splitters.bam /dev/stdin) \
--discordantFile >(gawk '{ if ($0~"^@") { print; next } else { $10="*"; $11="*"; print } }' OFS="\t" | \
$SAMBAMBA view -S -f bam /dev/stdin | \
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin
" | $PARALLEL -j 3
$SAMBAMBA sort -t 4 -m 1G --tmpdir=$TEMP_DIR/disc -o $OUTPUT.discordants.bam /dev/stdin) | \
$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
fi

# index the files
if [[ $VERBOSE -eq 1 ]]
then
Expand Down