Add option to output SAM header when querying BAM files

src/include/indexManagementBam.h

@@ -67,4 +67,4 @@ void saveBarcodesOffsetsIndex(BarcodesOffsetsIndex& index, string file);
 */
 BarcodesOffsetsIndex loadBarcodesOffsetsIndex(string file);
 
-#endif
+#endif

src/include/subcommands/help.h

@@ -3,7 +3,7 @@
 
 #include <string>
 
-#define VERSION "LRez v.2.1.1"
+#define VERSION "LRez v.2.1.2"
 
 using namespace std;
 

src/subcommands/help.cpp

@@ -85,6 +85,7 @@ void subcommandHelp(std::string subcommand) {
 		printf("\t-q, --query\t Query barcode to search in the BAM / index\n");
 		printf("\t-l, --list\t File containing a list of barcodes to search in the BAM / index\n");
 		printf("\t-o, --output\t File where to output the extracted alignments (optional, default: stdout)\n");
+		printf("\t-H, --header\t Output SAM header (optional, default: false)\n");
 	} else if (subcommand == "index fastq") {
 		printf("%s\n", VERSION);
 		printf("Pierre Morisse <[email protected]>\n");

src/subcommands/queryBam.cpp

@@ -12,19 +12,21 @@ void subcommandQueryBam(int argc, char* argv[]) {
 	string outputFile;
 	BarcodesOffsetsIndex BarcodesOffsetsIndex;
 	ofstream out;
+	bool outputHeader = false;
 
 	const struct option longopts[] = {
 		{"bam",				required_argument,	0, 'b'},
 		{"index",			required_argument,	0, 'i'},
 		{"query",			required_argument,	0, 'q'},
 		{"list",			required_argument,	0, 'l'},
 		{"output",			required_argument,	0, 'o'},
+		{"header",			no_argument,		0, 'H'},
 		{0, 0, 0, 0},
 	};
 	int index;
 	int iarg = 0;
 
-	iarg = getopt_long(argc, argv, "b:i:q:l:o:", longopts, &index);
+	iarg = getopt_long(argc, argv, "b:i:q:l:o:H", longopts, &index);
 	if (iarg == -1) {
 		subcommandHelp("query bam");
 	}
@@ -45,11 +47,14 @@ void subcommandQueryBam(int argc, char* argv[]) {
 			case 'o':
 				outputFile = optarg;
 				break;
+			case 'H':
+				outputHeader = true;
+				break;
 			default:
 				subcommandHelp("query bam");
 				break;
 		}
-		iarg = getopt_long(argc, argv, "b:i:q:l:o:", longopts, &index);
+		iarg = getopt_long(argc, argv, "b:i:q:l:o:H", longopts, &index);
 	}
 
 	if (bamFile.empty()) {
@@ -96,11 +101,17 @@ void subcommandQueryBam(int argc, char* argv[]) {
 			fprintf(stderr, "Unable to open file %s.", outputFile.c_str());
 			exit(EXIT_FAILURE);
 		}
+		if (outputHeader) {
+			out << reader.GetHeaderText() << endl;
+		}
 		for (BamAlignment al : alignments) {
 			out << convertToSam(al, reader.GetReferenceData()) << endl;
 		}
 		out.close();
 	} else {
+		if (outputHeader) {
+			cout << reader.GetHeaderText() << endl;
+		}
 		for (BamAlignment al : alignments) {
 			cout << convertToSam(al, reader.GetReferenceData()) << endl;
 		}