1.3.1

base.cpp

@@ -16,7 +16,7 @@ using namespace std;
 typedef uint32_t DepthType; // type for depth of coverage, kept it small
 const char ref_char = '>';  // reference prefix for "counts" output
 
-const string VERSION = "%prog 1.3.0"
+const string VERSION = "%prog 1.3.1"
 	"\nCopyright (C) 2014-2019 Giovanni Birolo and Andrea Telatin\n"
 	"https://github.com/telatin/covtobed - License MIT"
 	".\n"
@@ -105,8 +105,11 @@ struct Coverage {
 		else
 			--f;
 	}
-	bool operator==(const Coverage &o) const {
-		return f == o.f && r == o.r;
+	bool equal(const Coverage &o, bool stranded) const {
+	    	if (stranded)
+		    return f == o.f && r == o.r;
+		else
+		    return f + r == o.f + o.r;
 	}
 };
 
@@ -122,7 +125,7 @@ class Output {
 		// write interval to bed
 		void operator() (const Interval &i, const Coverage &c) {
 			// can the last interval be extended with the same coverage?
-			if (i.ref == last_interval.ref && i.start == last_interval.end && last_coverage == c)
+			if (i.ref == last_interval.ref && i.start == last_interval.end && last_coverage.equal(c, strands))
 				// extend previous interval
 				last_interval.end = i.end;
 			else {

test/test.sh

@@ -20,24 +20,30 @@ if [ ! -e "./covtobed" ]; then
 	if [ `uname` == 'Darwin' ]; then
 		echo " - Copying macOS binary"  || echo " ERROR: pre-compiled binary not working"
 		cp ./binaries/covtobed_mac ./covtobed
-		covtobed --version
+		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
 	else
 		echo " - Trying Ubuntu binary"
 		cp ./binaries/covtobed ./covtobed
-		covtobed --version || echo " ERROR: pre-compiled binary not working"
+		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
 	fi
 fi
 
 ./covtobed --version
 
+echo " ================================================ "
 set -eou pipefail
 # Compilation success, checking that --version emits the expected "progname" string
 echo -n " - Compiled binary prints version: "
-if [ $(./covtobed --version  | grep covtobed | wc -l ) -eq "1" ];
+if [ $(./covtobed --version  | grep covtobed | wc -l ) -gt "1" ];
 then
-        echo PASS 1
+        echo PASS $(./covtobed --version | grep covtobed |head -n 1)
+else
+        echo FAIL $(./covtobed --version  | grep covtobed | wc -l )
+		exit
 fi
 
+
+
 # Testing that -m MIN produces an output, and it fits the expectation for demo.bam (n. lines)
 echo -n " - Minimum coverage, expected BED lines check: "
 if [ $(./covtobed -m 15 test/demo.bam  | wc -l) -eq "12" ];
@@ -78,20 +84,28 @@ else
 	exit 1
 fi
 echo -n " - Testing 'counts' format (printed lines): "
-if [ $(./covtobed --format counts test/demo.bam | grep -v '>' | wc -l) -eq "202" ];
+if [ $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) -eq "202" ];
 then
         echo PASS 6
 else
-	echo FAIL
+	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
 	exit 1
 fi
 
+echo -n " - Testing strand with adjacent intervals: "
+if [[ $(./covtobed  test/stranded.bam | wc -l) -eq "1"  && $(./covtobed --output-strands test/stranded.bam | wc -l) -eq "2" ]];
+then
+        echo PASS 7
+else
+	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
+	exit 1
+fi
 # Checking BED output with reference output file
 echo -n " - Checking identity of BED output with pre-calculated: "
 ./covtobed test/demo.bam > test/output.test
 if [ $(diff test/output.test test/output.bed | wc -l) -eq "0" ];
 then
-        echo PASS 7
+        echo PASS 8
 	rm test/output.test
 else
 	echo FAIL
@@ -103,7 +117,7 @@ echo -n " - Checking computed coverage for a synthetic BAM file: "
 ./covtobed -m 1 test/mock.bam > test/output.test
 if [ $(diff test/output.test test/mock.bed | wc -l) -eq "0" ];
 then
-        echo PASS 8
+        echo PASS 9
 	rm test/output.test
 else
 	echo FAIL
@@ -113,7 +127,7 @@ fi
 ## Filter non valid alignments
 echo -n " - Checking filtering of invalid alignments: "
 if [ $(./covtobed -m 1 -d test/filtered.bam | wc -l) -eq "2" ] ; then
-	echo -n "PASS 9,"
+	echo -n "PASS 10,"
 else
 	echo FAIL
 	exit 1