Fix indexing bug with "placed" unmapped reads.

Unmapped-but-placed (having REF/POS) reads are not included in the
index.  Hence if an placed unmapped is the first record in a bin, then
it may not be returned.  Note most aligners write out mapped followed
by unmapped which does not trigger this problem.

The SAM spec states that all unmapped placed reads should be
considered as having an alignment length of 1.  While it doesn't seem
to explicitly state these must therefore be in the index, it does
imply it.  It appears that picard also indexes placed reads in this
manner.

Originally reported by John Marshall.  Fixes samtools#1142

hts.c

@@ -2384,14 +2384,12 @@ int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t
     if ( tid>=0 )
     {
         if (idx->bidx[tid] == 0) idx->bidx[tid] = kh_init(bin);
-        if (is_mapped) {
-            // shoehorn [-1,0) (VCF POS=0) into the leftmost bottom-level bin
-            if (beg < 0)  beg = 0;
-            if (end <= 0) end = 1;
-            // idx->z.last_off points to the start of the current record
-            if (insert_to_l(&idx->lidx[tid], beg, end,
-                            idx->z.last_off, idx->min_shift) < 0) return -1;
-        }
+        // shoehorn [-1,0) (VCF POS=0) into the leftmost bottom-level bin
+        if (beg < 0)  beg = 0;
+        if (end <= 0) end = 1;
+        // idx->z.last_off points to the start of the current record
+        if (insert_to_l(&idx->lidx[tid], beg, end,
+                        idx->z.last_off, idx->min_shift) < 0) return -1;
     }
     else idx->n_no_coor++;
     bin = hts_reg2bin(beg, end, idx->min_shift, idx->n_lvls);

test/index2.sam

@@ -0,0 +1,11 @@
+@HD	VN:1.4	SO:coordinate
+@SQ	SN:1	LN:249250621	M5:1b22b98cdeb4a9304cb5d48026a85128
+@SQ	SN:2	LN:243199373	M5:a0d9851da00400dec1098a9255ac712e
+um1	69	1	1000000	0	*	*	0	0	AAAAAAAAAA	*
+um1	137	1	1000000	44	10M	*	0	0	AAAAAAAAAA	*
+um2	69	1	2000000	0	*	*	0	0	AAAAAAAAAA	*
+um2	137	1	2000000	44	10M	*	0	0	AAAAAAAAAA	*
+mu1	137	2	1000000	44	10M	*	0	0	AAAAAAAAAA	*
+mu1	69	2	1000000	0	*	*	0	0	AAAAAAAAAA	*
+mu2	137	2	2000000	44	10M	*	0	0	AAAAAAAAAA	*
+mu2	69	2	2000000	0	*	*	0	0	AAAAAAAAAA	*

test/test.pl

@@ -840,6 +840,31 @@ sub test_index
         $wtmp =~ s/\//\\\\/g;
     }
     test_cmd($opts,out=>'tabix.out',cmd=>"$$opts{bin}/tabix $wtmp/index.vcf.gz##idx##$wtmp/index.vcf.gz.tbi 1:10000060-10000060");
+
+    cmd("$$opts{path}/test_view $$opts{path}/index2.sam -b -p $$opts{tmp}/index2.bam -x $$opts{tmp}/index2.bam.bai");
+    for (my $tid = 1; $tid <= 2; $tid++) {
+        for (my $pos = 1; $pos <= 2; $pos++) {
+            # All queries should return exactly two sequences.
+            # The input data consists of mapped/unmapped and unmapped/mapped
+            # in both orders.
+            # Done verbatim as test_cmd cannot return $out for us to check.
+            my $test = "$$opts{path}/test_view $$opts{tmp}/index2.bam $tid:${pos}000000-${pos}000000";
+            print "test_index:\n\t$test\n";
+            my ($ret, $out) = _cmd($test);
+            if ($ret ne 0) {
+                failed($opts, $test);
+            } else {
+                my $rnum = ($out =~ s/^[^@].*\n//gm);
+                if ($rnum ne 2) {
+                    failed($opts, $test);
+                } else {
+                    passed($opts, $test);
+                }
+            }
+        }
+    }
+    unlink("$$opts{tmp}/index2.bam");
+    unlink("$$opts{tmp}/index2.bam.bai");
 }
 
 sub test_bcf2vcf