Changed vector copies to references

src/sortBed/sortBed.cpp

@@ -40,7 +40,7 @@ void BedSort::SortBed() {
     for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
 
         // bedList is already sorted by start position.
-        vector<BED> bedList = m->second;
+        const vector<BED> &bedList = m->second;
 
         for (unsigned int i = 0; i < bedList.size(); ++i) {
             _bed->reportBedNewLine(bedList[i]);
@@ -105,7 +105,7 @@ void BedSort::SortBedOnFaidx()
 			if( m == _bed->bedMapNoBin.end() ) continue; //this chromosome is not present in BED
 			
 		    // bedList is already sorted by start position.
-		    vector<BED> bedList = m->second;
+		    const vector<BED> &bedList = m->second;
 
 		    for (unsigned int i = 0; i < bedList.size(); ++i) {
 		        _bed->reportBedNewLine(bedList[i]);
@@ -124,11 +124,11 @@ void BedSort::SortBedBySizeAsc() {
     for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
 
         // bedList is already sorted by start position.
-        vector<BED> bedList = m->second;
+        const vector<BED> &bedList = m->second;
 
         // add the entries from this chromosome to the current list
-        for (unsigned int i = 0; i < m->second.size(); ++i) {
-            masterList.push_back(m->second[i]);
+        for (unsigned int i = 0; i < bedList.size(); ++i) {
+            masterList.push_back(bedList[i]);
         }
     }
 
@@ -151,11 +151,11 @@ void BedSort::SortBedBySizeDesc() {
     for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
 
         // bedList is already sorted by start position.
-        vector<BED> bedList = m->second;
+        const vector<BED> &bedList = m->second;
 
         // add the entries from this chromosome to the current list
-        for (unsigned int i = 0; i < m->second.size(); ++i) {
-            masterList.push_back(m->second[i]);
+        for (unsigned int i = 0; i < bedList.size(); ++i) {
+            masterList.push_back(bedList[i]);
         }
     }
 
@@ -174,7 +174,7 @@ void BedSort::SortBedByChromThenSizeAsc() {
     for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
 
         // bedList is already sorted by start position.
-        vector<BED> bedList = m->second;
+        vector<BED> &bedList = m->second;
         sort(bedList.begin(), bedList.end(), sortBySizeAsc);
 
         for (unsigned int i = 0; i < bedList.size(); ++i) {
@@ -190,7 +190,7 @@ void BedSort::SortBedByChromThenSizeDesc() {
     for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
 
         // bedList is already sorted by start position.
-        vector<BED> bedList = m->second;
+        vector<BED> &bedList = m->second;
 
         sort(bedList.begin(), bedList.end(), sortBySizeDesc);
 
@@ -208,7 +208,7 @@ void BedSort::SortBedByChromThenScoreAsc() {
         for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
 
             // bedList is already sorted by start position.
-            vector<BED> bedList = m->second;
+            vector<BED> &bedList = m->second;
             sort(bedList.begin(), bedList.end(), sortByScoreAsc);
 
             for (unsigned int i = 0; i < bedList.size(); ++i) {
@@ -230,7 +230,7 @@ void BedSort::SortBedByChromThenScoreDesc() {
         for (masterBedMapNoBin::iterator m = _bed->bedMapNoBin.begin(); m != _bed->bedMapNoBin.end(); ++m) {
 
             // bedList is already sorted by start position.
-            vector<BED> bedList = m->second;
+            vector<BED> &bedList = m->second;
             sort(bedList.begin(), bedList.end(), sortByScoreDesc);
 
             for (unsigned int i = 0; i < bedList.size(); ++i) {

test/sort/a.bed

+#Header line for a.bed
+chr7	240	560	x	86	-
+chr7	210	525	d	21	+
+chr7	2100	2310	e	32	+
+chr3	40	260	p	41	-
+chr3	10	220	f	12	+
+chr3	100	320	g	96	-
+chr9	140	160	z	05	+
+chr9	110	120	a	81	-
+chr9	1100	1120	b	12	+
+

test/sort/names.txt

+chr9
+chr3
+chr7

test/sort/test-sort.sh

+BT=${BT-../../bin/bedtools}
+
+check()
+{
+	if diff $1 $2; then
+    	echo ok
+	else
+    	echo fail
+	fi
+}
+
+###########################################################
+#  Test default
+############################################################
+echo "    intersect.t01...\c"
+echo \
+"chr3	10	220	f	12	+
+chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr7	210	525	d	21	+
+chr7	240	560	x	86	-
+chr7	2100	2310	e	32	+
+chr9	110	120	a	81	-
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+" > exp
+$BT sort -i a.bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test sizeA
+############################################################
+echo "    intersect.t02...\c"
+echo \
+"chr9	110	120	a	81	-
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+
+chr3	10	220	f	12	+
+chr7	2100	2310	e	32	+
+chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr7	210	525	d	21	+
+chr7	240	560	x	86	-" > exp
+$BT sort -i a.bed -sizeA > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test sizeD
+############################################################
+echo "    intersect.t03...\c"
+echo \
+"chr7	240	560	x	86	-
+chr7	210	525	d	21	+
+chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr3	10	220	f	12	+
+chr7	2100	2310	e	32	+
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+
+chr9	110	120	a	81	-" > exp
+$BT sort -i a.bed -sizeD > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+#  Test chrThenSizeA
+############################################################
+echo "    intersect.t04...\c"
+echo \
+"chr3	10	220	f	12	+
+chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr7	2100	2310	e	32	+
+chr7	210	525	d	21	+
+chr7	240	560	x	86	-
+chr9	110	120	a	81	-
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+" > exp
+$BT sort -i a.bed -chrThenSizeA > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test chrThenSizeD
+############################################################
+echo "    intersect.t05...\c"
+echo \
+"chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr3	10	220	f	12	+
+chr7	240	560	x	86	-
+chr7	210	525	d	21	+
+chr7	2100	2310	e	32	+
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+
+chr9	110	120	a	81	-" > exp
+$BT sort -i a.bed -chrThenSizeD > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+#  Test chrThenScoreA
+############################################################
+echo "    intersect.t06...\c"
+echo \
+"chr3	10	220	f	12	+
+chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr7	210	525	d	21	+
+chr7	2100	2310	e	32	+
+chr7	240	560	x	86	-
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+
+chr9	110	120	a	81	-" > exp
+$BT sort -i a.bed -chrThenScoreA > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test chrThenScoreD
+############################################################
+echo "    intersect.t07...\c"
+echo \
+"chr3	100	320	g	96	-
+chr3	40	260	p	41	-
+chr3	10	220	f	12	+
+chr7	240	560	x	86	-
+chr7	2100	2310	e	32	+
+chr7	210	525	d	21	+
+chr9	110	120	a	81	-
+chr9	1100	1120	b	12	+
+chr9	140	160	z	05	+" > exp
+$BT sort -i a.bed -chrThenScoreD > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test faidx
+############################################################
+echo "    intersect.t08...\c"
+echo \
+"chr9	110	120	a	81	-
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+
+chr3	10	220	f	12	+
+chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr7	210	525	d	21	+
+chr7	240	560	x	86	-
+chr7	2100	2310	e	32	+" > exp
+$BT sort -i a.bed -faidx names.txt > obs
+check obs exp
+rm obs exp
+
+###########################################################
+#  Test header
+############################################################
+echo "    intersect.t09...\c"
+echo \
+"#Header line for a.bed
+chr3	10	220	f	12	+
+chr3	40	260	p	41	-
+chr3	100	320	g	96	-
+chr7	210	525	d	21	+
+chr7	240	560	x	86	-
+chr7	2100	2310	e	32	+
+chr9	110	120	a	81	-
+chr9	140	160	z	05	+
+chr9	1100	1120	b	12	+" > exp
+$BT sort -i a.bed -header > obs
+check obs exp
+rm obs exp
+

test/test.sh

@@ -52,6 +52,9 @@ cd reldist; bash test-reldist.sh; cd ..
 echo " Testing bedtools slop:"
 cd slop; bash test-slop.sh; cd ..
 
+echo " Testing bedtools sort:"
+cd slop; bash test-sort.sh; cd ..
+
 echo " Testing bedtools shuffle:"
 cd shuffle; bash test-shuffle.sh; cd ..