[CI] Add command in README

README.md

@@ -1,2 +1,25 @@
-# ALLHIC
-Genome scaffolding based on HiC data
+# ALLHIC Genome scaffolding based on HiC data
+
+## Usage
+
+### Partition
+
+Given a target k, number of partitions, the goal of the partitioning
+is to separate all the contigs into separate clusters. As with all
+clustering algorithm, there is an optimization goal here. The
+LACHESIS algorithm is a hierarchical clustering algorithm using
+average links.
+
+```bash
+allhic partition tests/prunning.sub.bam
+```
+
+### Optimize
+
+Given a set of Hi-C contacts between contigs, as specified in the
+clmfile, reconstruct the highest scoring ordering and orientations
+for these contigs.
+
+```bash
+allhic optimize tests/test.clm
+```

allhic/optimize.go

@@ -41,8 +41,11 @@ func (r *Optimizer) Run() {
 	}
 
 	for phase := 1; ; phase++ {
-		clm.OptimizeOrientations(fwtour, phase)
-		break
+		tag1, tag2 := clm.OptimizeOrientations(fwtour, phase)
+		if tag1 == REJECT && tag2 == REJECT {
+			log.Noticef("Terminating ... no more %v", ACCEPT)
+			break
+		}
 	}
 }
 
@@ -55,12 +58,12 @@ func (r *CLMFile) OptimizeOrdering(fwtour *os.File, phase int) {
 }
 
 // OptimizeOrientations changes the orientations of contigs by using heuristic flipping algorithms.
-func (r *CLMFile) OptimizeOrientations(fwtour *os.File, phase int) {
+func (r *CLMFile) OptimizeOrientations(fwtour *os.File, phase int) (string, string) {
 	tag1 := r.flipWhole()
 	r.PrintTour(fwtour, r.Tour, fmt.Sprintf("FLIPWHOLE%d", phase))
 	tag2 := r.flipOne()
 	r.PrintTour(fwtour, r.Tour, fmt.Sprintf("FLIPONE%d", phase))
-	fmt.Println(tag1, tag2)
+	return tag1, tag2
 }
 
 // PrintTour logs the current tour to file

allhic/orientation.go

@@ -53,7 +53,7 @@ func (r *CLMFile) flipAll() {
 
 // flipWhole test flipping all contigs at the same time to see if score improves
 func (r *CLMFile) flipWhole() (tag string) {
-	var oldSigns []byte
+	oldSigns := make([]byte, len(r.Signs))
 	copy(oldSigns, r.Signs)
 	score := r.EvaluateQ()
 
@@ -78,9 +78,6 @@ func (r *CLMFile) flipOne() (tag string) {
 	anyTagACCEPT := false
 	score := r.EvaluateQ()
 	for i, t := range r.Tour.Tigs {
-		if i == 0 {
-			continue
-		}
 		idx := t.Idx
 		r.Signs[idx] = rr(r.Signs[idx])
 		newScore := r.EvaluateQ()