test updates

ebwt.cpp

@@ -15,11 +15,11 @@ using namespace std;
 
 #ifdef BOWTIE_64BIT_INDEX
 
-std::string gEbwt_ext("bt2l");
+std::string gEbwt_ext("ebwtl");
 
 #else
 
-std::string gEbwt_ext("bt2");
+std::string gEbwt_ext("ebwt");
 
 #endif  // BOWTIE_64BIT_INDEX
 

ebwt_build.cpp

@@ -421,7 +421,7 @@ static void driver(const string& infile,
 				refparams.color = false;
 				vector<RefRecord> szs2;
 				vector<uint32_t> plens2;
-				int numSeqs2 = 0;
+				TIndexOff numSeqs2 = 0;
 				fastaRefReadSizes(is, szs2, plens2, refparams, NULL, numSeqs2);
 				assert_leq(numSeqs, numSeqs2);
 				// One less color than base

scripts/test/args.pl

@@ -8,7 +8,7 @@
 #
 
 my $bowtie = "./bowtie";
-my $bowtie_d = "./bowtie-debug";
+my $bowtie_build = "./bowtie-build";
 if(system("$bowtie --version") != 0) {
 	print STDERR "Could not execute ./bowtie; looking in PATH...\n";
 	$bowtie = `which bowtie`;
@@ -17,18 +17,9 @@
 		die "Could not find bowtie in current directory or in PATH\n";
 	}
 }
-if(system("$bowtie_d --version") != 0) {
-	print STDERR "Could not execute ./bowtie-debug; looking in PATH...\n";
-	$bowtie_d = `which bowtie-debug`;
-	chomp($bowtie_d);
-	if(system("$bowtie_d --version") != 0) {
-		die "Could not find bowtie-debug in current directory or in PATH\n";
-	}
-}
 
 if(! -f "e_coli_c.1.ebwt") {
 	print STDERR "Making colorspace e_coli index\n";
-	my $bowtie_build = "./bowtie-build";
 	if(system("$bowtie_build --version") != 0) {
 		print STDERR "Could not execute ./bowtie-build; looking in PATH...\n";
 		$bowtie_build = `which $bowtie_build`;
@@ -42,6 +33,12 @@
 	print STDERR "Colorspace e_coli index already present...\n";
 }
 
+if(! -f "e_coli.1.ebwt") {
+    system("$bowtie_build  genomes/NC_008253.fna e_coli") && die;
+} else {
+    print STDERR "e_coli index already present...\n";
+}
+
 open TMP, ">.args.pl.1.fa" || die;
 print TMP ">\nT0120012002012030303023\n";
 close(TMP);
@@ -98,24 +95,24 @@ ($)
 print "Bad:\n";
 for my $a (@bad) {
 	run("$bowtie $a e_coli reads/e_coli_1000.fq /dev/null") != 0 || die "bowtie should have rejected: \"$a\"\n";
-	run("$bowtie_d $a e_coli reads/e_coli_1000.fq /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
+	run("$bowtie --debug $a e_coli reads/e_coli_1000.fq /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
 	print "PASSED: bad args \"$a\"\n";
 }
 print "\nBadEx:\n";
 for my $a (@badEx) {
 	run("$bowtie $a  /dev/null") != 0 || die "bowtie should have rejected: \"$a\"\n";
-	run("$bowtie_d $a  /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
+	run("$bowtie --debug  $a  /dev/null") != 0 || die "bowtie-debug should have rejected: \"$a\"\n";
 	print "PASSED: bad args \"$a\"\n";
 }
 print "\nGood:\n";
 for my $a (@good) {
 	run("$bowtie $a e_coli reads/e_coli_1000.fq /dev/null") == 0 || die "bowtie should have accepted: \"$a\"\n";
-	run("$bowtie_d $a e_coli reads/e_coli_1000.fq /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
+	run("$bowtie --debug  $a e_coli reads/e_coli_1000.fq /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
 	print "PASSED: good args \"$a\"\n";
 }
 print "\nGoodEx:\n";
 for my $a (@goodEx) {
 	run("$bowtie $a /dev/null") == 0 || die "bowtie should have accepted: \"$a\"\n";
-	run("$bowtie_d $a /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
+	run("$bowtie --debug  $a /dev/null") == 0 || die "bowtie-debug should have accepted: \"$a\"\n";
 	print "PASSED: good args \"$a\"\n";
 }