From 491ff8feca2247d6d18f35da0484671505ab6f75 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Tue, 27 Apr 2021 08:50:34 -0700 Subject: [PATCH] Updating arcs-long with streaming reads (#111) * Stream reads from long-to-linked-pe to arcs --arks in long mode * Update min molecule size for arcs-long * Remove -g parameter for long-to-linked-pe --- Examples/arcs-make | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/Examples/arcs-make b/Examples/arcs-make index e76d3c2..6de10f3 100755 --- a/Examples/arcs-make +++ b/Examples/arcs-make @@ -255,14 +255,20 @@ else endif # long kmer -%_c$c_m$m_cut$(cut)_k$k_r$r_e$e_z$z_original.gv: %.renamed.fa $(reads).cut$(cut).fq.gz +$(reads).barcode-multiplicity.tsv: $(long_reads) + $(gtime) $(bin)/../src/long-to-linked-pe -l $(cut) -t $t -m2000 --bx-only -b $@ $< + +%_c$c_m$m_cut$(cut)_k$k_r$r_e$e_z$z_original.gv: %.renamed.fa $(long_reads) $(reads).barcode-multiplicity.tsv ifneq ($D, true) - $(gtime) arcs --arks -v -f $< -c $c -m $m -r $r -e $e -z $z -j $j -k $k -t $t -d $d --gap $(gap) -b $(patsubst %_original.gv,%,$@) $(word 2,$^) --barcode-counts $(barcode_counts).tsv + $(gtime) $(bin)/../src/long-to-linked-pe -l $(cut) -t $t -m2000 $(long_reads) |\ + arcs --arks -v -f $< -c $c -m $m -r $r -e $e -z $z -j $j -k $k -t $t -d $d --gap $(gap) -b $(patsubst %_original.gv,%,$@) -u $(reads).barcode-multiplicity.tsv /dev/stdin else ifneq ($(dist_upper), true) - $(gtime) arcs --arks -v -D -B $B -f $< -c $c -m $m -r $r -e $e -z $z -j $j -k $k -t $t -d $d --gap $(gap) -b $(patsubst %_original.gv,%,$@) $(word 2,$^) --barcode-counts $(barcode_counts).tsv + $(gtime) $(bin)/../src/long-to-linked-pe -l $(cut) -t $t -m2000 $(long_reads) |\ + arcs --arks -v -D -B $B -f $< -c $c -m $m -r $r -e $e -z $z -j $j -k $k -t $t -d $d --gap $(gap) -b $(patsubst %_original.gv,%,$@) -u $(reads).barcode-multiplicity.tsv /dev/stdin else - $(gtime) arcs --arks -v -D -B $B --dist_upper -f $< -c $c -m $m -r $r -e $e -z $z -j $j -k $k -t $t -d $d --gap $(gap) -b $(patsubst %_original.gv,%,$@) $(word 2,$^) --barcode-counts $(barcode_counts).tsv + $(gtime) $(bin)/../src/long-to-linked-pe -l $(cut) -t $t -m2000 $(long_reads) |\ + arcs --arks -v -D -B $B --dist_upper -f $< -c $c -m $m -r $r -e $e -z $z -j $j -k $k -t $t -d $d --gap $(gap) -b $(patsubst %_original.gv,%,$@) -u $(reads).barcode-multiplicity.tsv /dev/stdin endif # Generate TSV from ARCS