Don't drop in-flight decode jobs when seeking in cram_next_slice()

cram_next_slice() with a region set tries to skip over containers
with contents that don't overlap the region of interest.  For
files with a mixture of read lengths, it's possible that some
decode jobs have been queued before a later container is skipped.
This makes calling cram_seek() hazardous as it drops any in-flight
jobs before updating the file position.  Instead, call hseek()
directly so already-queued decode jobs are retained.

Author: daviesrob

Makefile

@@ -525,7 +525,7 @@ realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_sam_h)
 textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(htslib_sam_h) $(hts_internal_h)
 
 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(fuzz_settings_h) $(htslib_hts_endian_h) $(htscodecs_varint_h) $(htscodecs_pack_h) $(htscodecs_rle_h) $(cram_h)
-cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h)
+cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hfile_h)
 cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(sam_internal_h) $(htslib_hts_h) $(htslib_hts_endian_h) $(textutils_internal_h)
 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htscodecs_rANS_static4x16_h) $(htslib_hfile_h) $(cram_h)
 cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h)

cram/cram_decode.c

@@ -51,6 +51,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "cram.h"
 #include "os.h"
 #include "../htslib/hts.h"
+#include "../htslib/hfile.h"
 
 //Whether CIGAR has just M or uses = and X to indicate match and mismatch
 //#define USE_X
@@ -3287,14 +3288,18 @@ cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) {
                         break;
                     }
 
-                    // before start of range; skip to next container
+                    // Before start of range; skip to next container.
+                    // Can't use cram_seek() here as it drops in-progress
+                    // multi-threaded decode jobs, so call hseek() directly.
                     if (fd->range.refid != -1 &&
                         c_next->ref_seq_start + c_next->ref_seq_span-1 <
                         fd->range.start) {
-                        c_next->curr_slice_mt = c_next->max_slice;
-                        cram_seek(fd, c_next->length, SEEK_CUR);
+                        off_t skip_length = c_next->length;
                         cram_free_container(c_next);
                         c_next = NULL;
+                        fd->ooc = 0;
+                        if (hseek(fd->fp, skip_length, SEEK_CUR) < 0)
+                            return NULL;
                         continue;
                     }
                 }