Add tests for BAM alignment records that span BGZF blocks

HTSlib starts a new block if an alignment is likely to overflow
the current one, so for its own data this will only happen for
records longer than 64kbytes.  As other implementations may not do
this, check that reading works correctly on some BAM files where
records have been deliberately split between BGZF blocks.

Additionally, check the writing side by making a record with
enough CIGAR entries to make it split into multiple BGZF blocks.

.gitignore

@@ -45,6 +45,7 @@ shlib-exports-*.txt
 /bgzip
 /htsfile
 /tabix
+/test/bgzf_boundaries/*.tmp.*
 /test/faidx/*.tmp*
 /test/faidx/FAIL*
 /test/fieldarith

Makefile

@@ -914,6 +914,7 @@ htslib-uninstalled.pc: htslib.pc.tmp
 testclean:
 	-rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* test/faidx/FAIL* \
                test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* \
+               test/bgzf_boundaries/*.tmp.* \
                header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt
 	-rm -rf htscodecs/tests/test.out
 

test/test.pl

@@ -819,6 +819,43 @@ sub test_view
         }
     }
 
+    # BAM files with alignment records that span BGZF blocks
+    # HTSlib starts a new block if an alignment is likely to overflow the
+    # current one, so for its own data this will only happen for records
+    # longer than 64kbytes.  As other implementations may not do this,
+    # check that reading works correctly on some BAM files where records
+    # have been deliberately split between BGZF blocks.
+    print "test_view testing BAM records in multiple BGZF blocks:\n";
+    $test_view_failures = 0;
+    my $src_sam = "ce#1.sam";
+    foreach my $test_bam (qw(bgzf_boundaries/bgzf_boundaries1.bam
+                          bgzf_boundaries/bgzf_boundaries2.bam
+                          bgzf_boundaries/bgzf_boundaries3.bam)) {
+        testv $opts, "./test_view $tv_args -p $test_bam.tmp.sam $test_bam";
+        testv $opts, "./compare_sam.pl $test_bam.tmp.sam $src_sam";
+    }
+
+    # Test a file with a long alignment record.  Boundaries hit in the middle of
+    # the CIGAR data, and in the sequence.  Generate the test file here as it's
+    # big, but with fairly simple contents.
+    $src_sam = "bgzf_boundaries/large_rec.tmp.sam";
+    open(my $test_sam, '>', $src_sam) || die "Couldn't open $src_sam : $!\n";
+    print $test_sam "\@HD\tVN:1.6\tSO:coordinate\n";
+    print $test_sam "\@SQ\tSN:ref\tLN:100000\n";
+    print $test_sam "read\t0\tref\t1\t60\t", "1M1I" x 16000, "\t*\t0\t0\t", "A" x 32000, "\t", "Q" x 32000, "\n";
+    close($test_sam) || die "Error on closing $src_sam : $!\n";
+
+    testv $opts, "./test_view $tv_args -b -l 0 -p $src_sam.bam $src_sam";
+    testv $opts, "./test_view $tv_args -p $src_sam.bam.sam $src_sam.bam";
+    testv $opts, "./compare_sam.pl $src_sam $src_sam.bam.sam";
+
+    if ($test_view_failures == 0) {
+        passed($opts, "BAM records spanning multiple BGZF block tests");
+    } else {
+        failed($opts, "BAM records spanning multiple BGZF block tests",
+               "$test_view_failures subtests failed");
+    }
+
     # embed_ref=2 mode
     print "test_view testing embed_ref=2:\n";
     $test_view_failures = 0;