allow setting max depth

see #170

go.mod

@@ -0,0 +1,27 @@
+module github.com/brentp/smoove
+
+
+go 1.16
+
+require (
+	github.com/alexflint/go-arg v1.4.2
+	github.com/biogo/biogo v1.0.3 // indirect
+	github.com/biogo/hts v1.4.3
+	github.com/biogo/store v0.0.0-20201120204734-aad293a2328f
+	github.com/brentp/faidx v0.0.0-20200301150453-c39eb85760d8
+	github.com/brentp/gargs v0.3.9 // indirect
+	github.com/brentp/go-athenaeum v0.0.0-20180711164918-19f838fd53de
+	github.com/brentp/go-chartjs v0.0.0-20170901194241-a37b166b7875 // indirect
+	github.com/brentp/goleft v0.2.5
+	github.com/brentp/irelate v0.0.1 // indirect
+	github.com/brentp/vcfgo v0.0.0-20190824021612-654ed2e5945d
+	github.com/brentp/xopen v0.0.0-20181116180855-111b45cadc7d
+	github.com/edsrzf/mmap-go v1.0.0 // indirect
+	github.com/fatih/color v1.12.0 // indirect
+	github.com/kyroy/kdtree v0.0.0-20200419114247-70830f883f1d
+	github.com/mattn/go-isatty v0.0.13 // indirect
+	github.com/pkg/errors v0.9.1
+	github.com/valyala/fasttemplate v1.2.1
+	gonum.org/v1/gonum v0.9.3 // indirect
+	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c
+)

go.sum

@@ -0,0 +1,156 @@
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lumpy/lumpy.go

@@ -107,6 +107,20 @@ type cmdCounts struct {
 	mapCounts map[string][4]int
 }
 
+func getMaxDepth() int {
+	defaultD := 1000
+	t := os.Getenv("SMOOVE_MAX_DEPTH")
+	if t == "" {
+		return defaultD
+	}
+	n, err := strconv.Atoi(t)
+	if err != nil {
+		return defaultD
+	}
+	shared.Slogger.Printf("couldn't set max depth to %v", t)
+	return n
+}
+
 func Lumpy(project, reference string, outdir string, bam_paths []string, pool *shpool.Pool, exclude_bed string, filter_chroms []string, extraFilters bool, minWeight int) cmdCounts {
 	if pool == nil {
 		pool = shpool.New(runtime.GOMAXPROCS(0), nil, &shpool.Options{LogPrefix: shared.Prefix})
@@ -127,7 +141,9 @@ func Lumpy(project, reference string, outdir string, bam_paths []string, pool *s
 		panic(err)
 	}
 
-	mapCounts := remove_sketchy_all(filters, 1000, reference, exclude_bed, filter_chroms, extraFilters)
+	var maxDepth = getMaxDepth()
+
+	mapCounts := remove_sketchy_all(filters, maxDepth, reference, exclude_bed, filter_chroms, extraFilters)
 	shared.Slogger.Print("starting lumpy")
 	p := run_lumpy(filters, reference, outdir, false, project, minWeight)
 	return cmdCounts{cmd: p, mapCounts: mapCounts}

smoove.go

@@ -1,3 +1,3 @@
 package smoove
 
-const Version = "0.2.7"
+const Version = "0.2.8"