Add CRAM container skipping test

The test creates a CRAM file with records in lots of containers,
many of which should be skipped when making a region query that
expects to return the first and last two records in the file.

Author: daviesrob

test/index3.sam

@@ -0,0 +1,17 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:CHROMOSOME_I	LN:1009800	M5:8ede36131e0dbf3417807e48f77f3ebd
+@CO	CRAM container skipping test - very long reads followed by short ones.
+@CO	Use option seqs_per_slice=2 when writing CRAM so that records are
+@CO	stored in multiple containers.
+r0-1	0	CHROMOSOME_I	1	50	10000M	*	0	0	*	*
+r0-2	0	CHROMOSOME_I	1	50	10000M	*	0	0	*	*
+r1-1	0	CHROMOSOME_I	1000	50	100M	*	0	0	*	*
+r1-2	0	CHROMOSOME_I	1000	50	100M	*	0	0	*	*
+r2-1	0	CHROMOSOME_I	2000	50	100M	*	0	0	*	*
+r2-2	0	CHROMOSOME_I	2000	50	100M	*	0	0	*	*
+r3-1	0	CHROMOSOME_I	3000	50	100M	*	0	0	*	*
+r3-2	0	CHROMOSOME_I	3000	50	100M	*	0	0	*	*
+r4-1	0	CHROMOSOME_I	4000	50	100M	*	0	0	*	*
+r4-2	0	CHROMOSOME_I	4000	50	100M	*	0	0	*	*
+r5-1	0	CHROMOSOME_I	5000	50	100M	*	0	0	*	*
+r5-2	0	CHROMOSOME_I	5000	50	100M	*	0	0	*	*

test/index3_exp.sam

@@ -0,0 +1,9 @@
+@HD	VN:1.6	SO:coordinate
+@SQ	SN:CHROMOSOME_I	LN:1009800	M5:8ede36131e0dbf3417807e48f77f3ebd
+@CO	CRAM container skipping test - very long reads followed by short ones.
+@CO	Use option seqs_per_slice=2 when writing CRAM so that records are
+@CO	stored in multiple containers.
+r0-1	0	CHROMOSOME_I	1	50	10000M	*	0	0	*	*
+r0-2	0	CHROMOSOME_I	1	50	10000M	*	0	0	*	*
+r5-1	0	CHROMOSOME_I	5000	50	100M	*	0	0	*	*
+r5-2	0	CHROMOSOME_I	5000	50	100M	*	0	0	*	*

test/test.pl

@@ -1089,6 +1089,18 @@ sub test_index
     unlink("$$opts{tmp}/index.cram.crai");
     test_compare($opts,"$$opts{path}/test_index $$opts{tmp}/index.cram", "$$opts{tmp}/index.cram.crai", "$$opts{path}/index.cram.crai", gz=>1);
 
+    # CRAM container skipping test
+    # Prepare a file with records split into multiple containers, the first two
+    # records spanning far enough to overlap the last two.
+    cmd("$$opts{path}/test_view $nthreads -C -p $$opts{tmp}/index3.cram -x $$opts{tmp}/index3.cram.crai -o seqs_per_slice=2 $$opts{path}/index3.sam");
+    # An index lookup for the last two records should return the first two
+    # as well.
+    test_compare($opts, "$$opts{path}/test_view $nthreads -p $$opts{tmp}/index3_rgn.sam $$opts{tmp}/index3.cram CHROMOSOME_I:5000-5100",
+                 "$$opts{path}/index3_exp.sam", "$$opts{tmp}/index3_rgn.sam");
+    # Also check the multi-region iterator
+    test_compare($opts, "$$opts{path}/test_view $nthreads -M -p $$opts{tmp}/index3_rgnm.sam $$opts{tmp}/index3.cram CHROMOSOME_I:5000-5100",
+                 "$$opts{path}/index3_exp.sam", "$$opts{tmp}/index3_rgnm.sam");
+
     # BCF
     test_compare($opts,"$$opts{path}/test_view $nthreads -l 0 -b -m 14 -x $$opts{tmp}/index.bcf.csi $$opts{path}/index.vcf > $$opts{tmp}/index.bcf", "$$opts{tmp}/index.bcf.csi", "$$opts{path}/index.bcf.csi", gz=>1);
     unlink("$$opts{tmp}/index.bcf.csi");