[allhic] Use logging in partition

allhic/clm.go

@@ -130,3 +130,16 @@ func (r *CLMFile) ParseClm() {
 		// fmt.Println(contact.a, contact.b, contact.nlinks, strandedness)
 	}
 }
+
+// tigToIdx maps tigs to indices in the current active tigs
+func (r *CLMFile) tigToIdx() map[string]int {
+	m := make(map[string]int)
+
+	return m
+}
+
+// M yields a contact frequency matrix, where each cell contains how many
+// links between i-th and j-th contig
+func (r *CLMFile) M() {
+
+}

allhic/partition.go

@@ -14,9 +14,9 @@ type Partitioner struct {
 }
 
 // CountLinks provides the method to count the links
-func (p Partitioner) CountLinks() {
-	fmt.Println("In CountLinks()")
-	fh, err := os.Open(p.Bamfile)
+func (r Partitioner) CountLinks() {
+	fh, err := os.Open(r.Bamfile)
+	log.Noticef("Parse bamfile `%s`", r.Bamfile)
 	if err != nil {
 		panic(err)
 	}

main.go

@@ -1,8 +1,6 @@
 package main
 
 import (
-	"fmt"
-
 	"./allhic"
 
 	"github.com/docopt/docopt-go"
@@ -27,7 +25,6 @@ Options:
 
 	if arguments["partition"].(bool) {
 		p := allhic.Partitioner{"tests/prunning.sub.bam"}
-		fmt.Println(p.Bamfile)
 		p.CountLinks()
 	} else if arguments["optimize"].(bool) {
 		p := allhic.Optimizer{"tests/test.clm"}