Fix bug when the total number of regions is too low

morispi · Sep 8, 2021 · ee19cef · ee19cef
1 parent 1cc1c42
commit ee19cef
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/src/subcommands/help.cpp b/src/subcommands/help.cpp
@@ -139,7 +139,7 @@ void subcommandHelp(std::string subcommand) {
 		printf("ARGS:\n");
 		printf("\t-b, --bam\t BAM file to retrieve stats from\n");
 		printf("\t-r, --regions\t Number of regions to consider to define stats (optional, default: 1000)\n");
-		printf("\t-s, --size\t Size of the regions to consider (optional, default: 10000) \n");
+		printf("\t-s, --size\t Size of the regions to consider (optional, default: 1000) \n");
 		printf("\t-o, --output\t File where to output the extracted reads (optional, default: stdout)\n");
 		printf("\t-t, --threads\t Number of threads to use when comparing a list of contigs (optional, default: 1)\n");
 	}

diff --git a/src/subcommands/stats.cpp b/src/subcommands/stats.cpp
@@ -72,7 +72,7 @@ void subcommandStats(int argc, char* argv[]) {
 
 		reader.Close();
 
-		pair<vector<unsigned>, vector<unsigned>> res = extractBarcodesAndCommonBarcodesCounts(bamFile, regionsList, numberOfRegions, nbThreads);
+		pair<vector<unsigned>, vector<unsigned>> res = extractBarcodesAndCommonBarcodesCounts(bamFile, regionsList, min(numberOfRegions, (unsigned) regionsList.size()), nbThreads);
 		vector<unsigned> barcodesPerRegion = res.first;
 		vector<unsigned> commonBarcodes = res.second;