[allhic] Make a copy before sort in median()

base.go

@@ -121,8 +121,12 @@ func min(a, b int) int {
 }
 
 // median gets the median value of an array
-func median(numbers []float64) float64 {
+func median(s []float64) float64 {
+	// Make a sorted copy
+	numbers := make([]float64, len(s))
+	copy(numbers, s)
 	sort.Float64s(numbers)
+
 	middle := len(numbers) / 2
 	result := numbers[middle]
 	if len(numbers)%2 == 0 {

clm.go

@@ -11,7 +11,6 @@ package allhic
 
 import (
 	"bufio"
-	"fmt"
 	"math"
 	"os"
 	"path"
@@ -214,8 +213,10 @@ func (r *CLMFile) pruneByDensity() {
 			invalid++
 		}
 	}
-	log.Noticef("Inactivated %d tigs with log10_density < %.5f",
-		invalid, lb)
+	if invalid > 0 {
+		log.Noticef("Inactivated %d tigs with log10_density < %.5f",
+			invalid, lb)
+	}
 }
 
 // pruneBySize selects active contigs based on size
@@ -227,8 +228,10 @@ func (r *CLMFile) pruneBySize() {
 			invalid++
 		}
 	}
-	log.Noticef("Inactivated %d tigs with size < %d",
-		invalid, MINSIZE)
+	if invalid > 0 {
+		log.Noticef("Inactivated %d tigs with size < %d",
+			invalid, MINSIZE)
+	}
 }
 
 // pruneTour test deleting each contig and check the delta_score
@@ -238,7 +241,7 @@ func (r *CLMFile) pruneTour() {
 		tour, newTour Tour
 	)
 
-	for phase := 1; phase < 3; phase++ {
+	for {
 		tour = r.Tour
 		tourScore := -tour.Evaluate()
 		log.Noticef("Starting score: %.5f", tourScore)
@@ -265,7 +268,7 @@ func (r *CLMFile) pruneTour() {
 		}
 		// Wait for all workers to finish
 		wg.Wait()
-		fmt.Println(log10ds)
+		//fmt.Println(log10ds)
 
 		// Identify outliers
 		lb, ub := OutlierCutoff(log10ds)
@@ -311,7 +314,7 @@ func (r *CLMFile) pruneTour() {
 func (r *CLMFile) Activate(shuffle bool) {
 	r.reportActive()
 	r.pruneByDensity()
-	r.pruneBySize()
+	//r.pruneBySize()
 	r.reportActive()
 
 	for _, tig := range r.Tigs {

evaluate.go

@@ -228,7 +228,7 @@ func (r *CLMFile) GARun(fwtour *os.File, npop, ngen int, mutrate float64, phase
 	for ; ; gen++ {
 		ga.Evolve()
 		currentBest := -ga.HallOfFame[0].Fitness
-		if gen%npop == 0 {
+		if gen%(ngen/10) == 0 {
 			fmt.Printf("Current iteration GA%d-%d: max_score=%.5f\n",
 				phase, gen, currentBest)
 			currentBestTour := ga.HallOfFame[0].Genome.(Tour)

functional-tests.sh

@@ -5,7 +5,7 @@ test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest
 . ssshtest
 set -uo pipefail
 
-go build -o allhic_test main/allhic.go
+go build -o allhic_test cmd/allhic.go
 
 run test_optimize ./allhic_test optimize tests/test.clm
 assert_in_stderr "Success"

optimize.go

@@ -52,7 +52,7 @@ func (r *Optimizer) Run() {
 
 // OptimizeOrdering changes the ordering of contigs by Genetic Algorithm
 func (r *CLMFile) OptimizeOrdering(fwtour *os.File, phase int) {
-	r.GARun(fwtour, 100, 2000, .2, phase)
+	r.GARun(fwtour, 100, 5000, .25, phase)
 	r.pruneTour()
 }