Added version and test files

Author: pjotrp

Makefile

@@ -65,6 +65,9 @@ tabix++: $(OBJS) main.cpp $(HTS_LIB)
 	$(CXX) $(CXXFLAGS) -o $@ main.cpp $(OBJS) $(INCLUDES) $(LIBPATH) \
 		-lhts -lpthread -lm -lz -lcurl -llzma -lbz2
 
+test: all
+	./tabix++ test/vcf_file.vcf.gz
+
 install: all
 	$(MKDIR) $(DESTDIR)$(PREFIX)/bin
 	$(MKDIR) $(DESTDIR)$(PREFIX)/include

README.md

@@ -5,6 +5,7 @@ This is a C++ wrapper around [tabix project](http://samtools.sourceforge.net/tab
 ```sh
 git submodule update --init --recursive
 make CC=gcc -j 16
+make test
 ```
 
 See also [guix.scm](./guix.scm) for the build environment we test with.

main.cpp

@@ -3,13 +3,16 @@
 
 using namespace std;
 
+const string VERSION = "1.1.1";
+
 int main(int argc, char** argv) {
 
     if (argc < 2) {
-        cerr << argv[0] << " [file] [ [region] ... ]" << endl
+        cout << argv[0] << " [file] [ [region] ... ]" << endl
              << "Writes out regions from bgzf-compressed, tabix-indexed file." << endl
              << "Supply 'header' to print out the header, and no regions to" << endl
-             << "print the contents of the entire file." << endl;
+             << "print the contents of the entire file." << endl << endl
+             << "Version " << VERSION << endl;
         return 1;
     }
 
@@ -22,7 +25,7 @@ int main(int argc, char** argv) {
     Tabix file(filename);
 
     if (!regions.empty()) {
-        for (vector<string>::iterator r = regions.begin(); r != regions.end(); ++r) { 
+        for (vector<string>::iterator r = regions.begin(); r != regions.end(); ++r) {
             string& region = *r;
             if (region == "header") {
                 string header;

tabix.cpp

@@ -13,26 +13,31 @@ Tabix::Tabix(string& file) {
     char *fnidx = (char*) calloc(strlen(cfilename) + 5, 1);
     strcat(strcpy(fnidx, cfilename), ".tbi");
 
-    hFILE *fp = hopen(cfilename, "r");
-    if (fp == NULL) {
+    hFILE *fp;
+    if (!(fp = hopen(cfilename, "r"))) {
       cerr << "can't open " << cfilename;
       return;
     }
 
     htsFormat fmt;
-    if ( hts_detect_format(fp,&fmt)!=1 )
+    if ( hts_detect_format(fp,&fmt) < 0 )
     {
         cerr << "[tabix++] was bgzip used to compress this file? " << file << endl;
         free(fnidx);
         exit(1);
     }
-    hclose(fp);
+    if (hclose(fp) != 0) {
+        cerr << "can't close " << cfilename;
+        return;
+    }
+
     // Common source of errors: new VCF is used with an old index
     stat(fnidx, &stat_tbi);
     stat(cfilename, &stat_vcf);
     if ( stat_vcf.st_mtime > stat_tbi.st_mtime )
     {
         cerr << "[tabix++] the index file is older than the vcf file. Please use '-f' to overwrite or reindex." << endl;
+
         free(fnidx);
         exit(1);
     }