segfault

test/read_bam_file.d

@@ -38,70 +38,70 @@ import std.regex;
 
 void main() {
 
-    auto bam = new BamReader("test/data/ex1_header.bam");
-    auto reads = bam["chr2"][150 .. 160]; // region chr2:149-158
-    auto pileup = makePileup(reads,
-            false,     // reads don't contain MD tags
-            155, 158); // specify [start, end) interval
+  auto bam = new BamReader("test/data/ex1_header.bam");
+  auto reads = bam["chr2"][150 .. 160]; // region chr2:149-158
+  auto pileup = makePileup(reads,
+                           false,     // reads don't contain MD tags
+                           155, 158); // specify [start, end) interval
 
-    foreach (column; pileup) {
-        writeln("Reference position: ", column.position);
-        writeln("    Coverage: ", column.coverage);
-        writeln("    Reads:");
+  foreach (column; pileup) {
+    writeln("Reference position: ", column.position);
+    writeln("    Coverage: ", column.coverage);
+    writeln("    Reads:");
 
-        foreach (read; column.reads) {
-            writefln("%30s\t%s\t%.2d\t%s\t%2s/%2s\t%2s/%2s\t%10s\t%s %s",
-                    read.name,
-                    read.current_base,
-                    read.current_base_quality,
-                    read.cigar_operation,
-                    read.cigar_operation_offset + 1, read.cigar_operation.length,
-                    read.query_offset + 1, read.sequence.length,
-                    read.cigarString(),
-                    read.cigar_before, read.cigar_after);
-        }
+    foreach (read; column.reads) {
+      writefln("%30s\t%s\t%.2d\t%s\t%2s/%2s\t%2s/%2s\t%10s\t%s %s",
+               read.name,
+               read.current_base,
+               read.current_base_quality,
+               read.cigar_operation,
+               read.cigar_operation_offset + 1, read.cigar_operation.length,
+               read.query_offset + 1, read.sequence.length,
+               read.cigarString(),
+               read.cigar_before, read.cigar_after);
     }
+  }
 
- {
-   auto fn = buildPath(dirName(__FILE__), "data", "b.sam");
-   auto sam = new SamReader(fn);
-   auto writer = new BamWriter("/dev/null", 0);
-   writer.writeSamHeader(sam.header);
-   writer.writeReferenceSequenceInfo(sam.reference_sequences);
-   foreach (r; sam.reads)
-     writer.writeRecord(r);
-   writer.finish();
- }
- {
-   auto fn = buildPath(dirName(__FILE__), "data", "bins.bam");
-   auto bf = new BamReader(fn);
- }
-   import core.memory;
-   stderr.writeln("**** Calling GC");
-   GC.collect();
-   stderr.writeln("**** Past calling GC");
- {
+  {
+    auto fn = buildPath(dirName(__FILE__), "data", "b.sam");
+    auto sam = new SamReader(fn);
+    auto writer = new BamWriter("/dev/null", 0);
+    writer.writeSamHeader(sam.header);
+    writer.writeReferenceSequenceInfo(sam.reference_sequences);
+    foreach (r; sam.reads)
+      writer.writeRecord(r);
+    writer.finish();
+  }
+  {
+    auto fn = buildPath(dirName(__FILE__), "data", "bins.bam");
+    auto bf = new BamReader(fn);
+  }
+  import core.memory;
+  stderr.writeln("**** Calling GC");
+  GC.collect();
+  stderr.writeln("**** Past calling GC");
+  {
 
-   auto fn = buildPath(dirName(__FILE__), "data", "ex1_header.bam");
-   auto bf = new BamReader(fn);
-   assert(bf.header.format_version == "1.3");
-   assert(bf.header.sorting_order == SortingOrder.coordinate);
-   assert(bf.header.sequences.length == 2);
-   assert(bf.header.getSequenceIndex("chr1") == 0);
-   assert(bf.header.sequences["chr2"].length == 1584);
+    auto fn = buildPath(dirName(__FILE__), "data", "ex1_header.bam");
+    auto bf = new BamReader(fn);
+    assert(bf.header.format_version == "1.3");
+    assert(bf.header.sorting_order == SortingOrder.coordinate);
+    assert(bf.header.sequences.length == 2);
+    assert(bf.header.getSequenceIndex("chr1") == 0);
+    assert(bf.header.sequences["chr2"].length == 1584);
 
-   auto fn2 = buildPath(dirName(__FILE__), "data", "bins.bam");
-   auto bf2 = new BamReader(fn2);
-   assert(bf2.header.sorting_order == SortingOrder.unknown);
-   assert(bf2.header.sequences.length == 3);
-   assert(bf2.header.read_groups.length == 0);
-   assert(bf2.header.getSequenceIndex("large") == 2);
-   assert(bf2.header.sequences["small"].length == 65536);
- }
+    auto fn2 = buildPath(dirName(__FILE__), "data", "bins.bam");
+    auto bf2 = new BamReader(fn2);
+    assert(bf2.header.sorting_order == SortingOrder.unknown);
+    assert(bf2.header.sequences.length == 3);
+    assert(bf2.header.read_groups.length == 0);
+    assert(bf2.header.getSequenceIndex("large") == 2);
+    assert(bf2.header.sequences["small"].length == 65536);
+  }
 
- // Time to kick in GC
- import core.memory;
- stderr.writeln("**** Calling GC");
- GC.collect();
- stderr.writeln("**** Past calling GC");
+  // Time to kick in GC
+  import core.memory;
+  stderr.writeln("**** Calling GC");
+  GC.collect();
+  stderr.writeln("**** Past calling GC");
 }