update mosdepth to use --fast-mode from latest version

brentp · Nov 19, 2018 · 6fda101 · 6fda101
1 parent 5e8a1b9
commit 6fda101
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 11 deletions.
diff --git a/HISTORY.md b/HISTORY.md
@@ -12,6 +12,7 @@ v0.2.2
   to use as-is.
 + cnvnator changes and filtering. (still requires github.com/brentp/CNVnator fork).
 + bugfix for case when no output directory was specified.
++ use mosdepth with --fast-mode **NOTE** this requires the latest version of mosdepth (0.2.4 or greater)
 
 v0.2.1
 ======

diff --git a/docker/docker-build.sh b/docker/docker-build.sh
@@ -86,10 +86,10 @@ cd svtools && python setup.py install
 cd $basedir
 rm -rf svtools
 
-wget -qO /usr/local/bin/mosdepth https://github.com/brentp/mosdepth/releases/download/v0.2.3/mosdepth
+wget -qO /usr/local/bin/mosdepth https://github.com/brentp/mosdepth/releases/download/v0.2.4/mosdepth
 chmod +x /usr/local/bin/mosdepth
 
-wget -qO /usr/local/bin/duphold https://github.com/brentp/duphold/releases/download/v0.0.9/duphold
+wget -qO /usr/local/bin/duphold https://github.com/brentp/duphold/releases/download/v0.1.0/duphold
 chmod +x /usr/local/bin/duphold
 
 wget -qO /usr/bin/gsort https://github.com/brentp/gsort/releases/download/v0.0.6/gsort_linux_amd64

diff --git a/lumpy/depthfilter.go b/lumpy/depthfilter.go
@@ -182,7 +182,7 @@ export MOSDEPTH_Q0=OK
 export MOSDEPTH Q1=HIGH
 set -euo pipefail
 samtools index {{bam}}
-mosdepth -f {{fasta}} -n --quantize {{md1}}: {{prefix}} {{bam}}
+mosdepth -f {{fasta}} --fast-mode -n --quantize {{md1}}: {{prefix}} {{bam}}
 rm -f {{prefix}}.mosdepth*.dist.txt
 rm {{prefix}}.quantized.bed.gz.csi
 `
@@ -376,28 +376,28 @@ type inter struct {
 	read2_tid uint32
 	read1_pos uint32
 	read2_pos uint32
-	qname string
-	retain bool
+	qname     string
+	retain    bool
 }
 
 // Size around an interchromosomal to look for support during filtering
 const inter_window_size = 10000
 const empty_tid = math.MaxUint32
 
 func localRightOutOfWindow(i, k inter) bool {
-	return (k.read1_tid > i.read1_tid || (k.read1_tid == i.read1_tid && k.read1_pos > i.read1_pos + inter_window_size))
+	return (k.read1_tid > i.read1_tid || (k.read1_tid == i.read1_tid && k.read1_pos > i.read1_pos+inter_window_size))
 }
 
 func localLeftOutOfWindow(i, k inter) bool {
-	return (k.read1_tid < i.read1_tid || (k.read1_tid == i.read1_tid && k.read1_pos < i.read1_pos - inter_window_size))
+	return (k.read1_tid < i.read1_tid || (k.read1_tid == i.read1_tid && k.read1_pos < i.read1_pos-inter_window_size))
 }
 
 func distantRightOutOfWindow(i, k inter) bool {
-	return (k.read2_tid > i.read2_tid || (k.read2_tid == i.read2_tid && k.read2_pos > i.read2_pos + inter_window_size))
+	return (k.read2_tid > i.read2_tid || (k.read2_tid == i.read2_tid && k.read2_pos > i.read2_pos+inter_window_size))
 }
 
 func distantLeftOutOfWindow(i, k inter) bool {
-	return (k.read2_tid < i.read2_tid || (k.read2_tid == i.read2_tid && k.read2_pos < i.read2_pos - inter_window_size))
+	return (k.read2_tid < i.read2_tid || (k.read2_tid == i.read2_tid && k.read2_pos < i.read2_pos-inter_window_size))
 }
 
 func interSlicePtrs(s []inter, d []*inter) []*inter {
@@ -412,7 +412,7 @@ func interchromfilter(counts map[string]int, inters []inter) {
 	for f := 0; f < len(inters); {
 		g := sort.Search(len(inters), func(z int) bool { return localRightOutOfWindow(inters[f], inters[z]) })
 		// now we know that everything between first and g is in-window relative to first
-		if f + 1 != g {
+		if f+1 != g {
 			// Need to check and see if in-window on distal site
 			// populate buf with pointers to elements so we don't mess up the initial array
 			buf = buf[:0]
@@ -428,7 +428,7 @@ func interchromfilter(counts map[string]int, inters []inter) {
 			})
 			for j := 0; j < len(buf); {
 				c := sort.Search(len(buf), func(z int) bool { return distantRightOutOfWindow(*buf[j], *buf[z]) })
-				if j + 1 != c {
+				if j+1 != c {
 					for i := j; i < c; i++ {
 						buf[i].retain = true
 					}