segfault

test/read_bam_file.d

@@ -147,73 +147,6 @@ CigarOperation[] cigarFromString(string cigar) {
     assert(bf.header.getSequenceIndex("large") == 2);
     assert(bf.header.sequences["small"].length == 65536);
 
-    // Time to kick in GC
-    import core.memory;
-    stderr.writeln("**** Calling GC");
-    GC.collect();
-    stderr.writeln("**** Past calling GC");
-
-    {
-    // stderr.writeln("Testing alignment parsing...");
-    fn = buildPath(dirName(__FILE__), "data", "ex1_header.bam");
-    bf = new BamReader(fn);
-    auto reads2 = bf.reads;
-    auto read = reads2.front;
-    assert(equal(read.sequence, "CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA"));
-    assert(equal(map!"cast(char)(a + 33)"(read.base_qualities),
-                "<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;"));
-    assert(bf.reference(read.ref_id).name == "chr1");
-    assert(read.name == "EAS56_57:6:190:289:82");
-    assert(read.flag == 69);
-    assert(read.position == 99);
-    assert(read.mapping_quality == 0);
-    reads2.popFront();
-    reads2.popFront();
-    assert(reads2.front.cigarString() == "35M");
-    assert(reads2.front.to!string() == "EAS51_64:3:190:727:308	99	chr1	103	99	35M	=	263	195	GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG	<<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844	MF:i:18	Aq:i:73	NM:i:0	UQ:i:0	H0:i:1	H1:i:0");
-    assert(bf.header.getSequenceIndex("chr1") == read.ref_id);
-    }
-
-    assert(bf.reads.front.name == "EAS56_57:6:190:289:82");
-    stderr.writeln("**** Calling GCx");
-    GC.collect();
-    stderr.writeln("**** Past calling GCx");
-
-    // stderr.writeln("Testing tag parsing...");
-    fn = buildPath(dirName(__FILE__), "data", "tags.bam");
-    bf = new BamReader(fn);
-    foreach (alignment; bf.reads) {
-        auto name = alignment.name;
-        assert(name[0..4] == "tag_");
-        char[] tag;
-        name = name[4..$];
-        while (name[0] != ':') {
-            tag ~= name[0];
-            name = name[1..$];
-        }
-        name = name[1..$];
-        auto value = alignment[tag.idup].toSam();
-        if (name != value) {
-            stderr.writeln("tag: ", tag, "\tname: ", name, "\tvalue: ", value);
-            stderr.writeln("value bam_typeid: ", alignment[tag.idup].bam_typeid);
-        }
-
-        assert(name == value);
-    }
-
-    // stderr.writeln("Testing exception handling...");
-    fn = buildPath(dirName(__FILE__), "data", "duplicated_block_size.bam");
-    assertThrown!BgzfException(new BamReader(fn));
-    fn = buildPath(dirName(__FILE__), "data", "no_block_size.bam");
-    assertThrown!BgzfException(new BamReader(fn));
-    fn = buildPath(dirName(__FILE__), "data", "wrong_extra_gzip_length.bam");
-    assertThrown!BgzfException(new BamReader(fn));
-    fn = buildPath(dirName(__FILE__), "data", "wrong_bc_subfield_length.bam");
-    assertThrown!BgzfException(reduce!"a+b.sequence_length"(0, (new BamReader(fn)).reads!withoutOffsets));
-    fn = buildPath(dirName(__FILE__), "data", "corrupted_zlib_archive.bam");
-    import bio.core.utils.zlib;
-    assertThrown!ZlibException(walkLength((new BamReader(fn)).reads));
-    // stderr.writeln("Testing random access...");
 
 
   }