More tweaks to cram threading.

The previous commit, while valid, also revealed more woes of multi-slice
containers, specifically when cancelling the current read by seeking
(draining the read-ahead decode queue).

Author: jkbonfield

cram/cram_decode.c

@@ -3150,22 +3150,23 @@ static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) {
 		if (s_next->hdr->ref_seq_id != fd->range.refid) {
 		    fd->ooc = 1;
 		    cram_free_slice(s_next);
-		    s_next = NULL;
+		    c_next->slice = s_next = NULL;
 		    break;
 		}
 
 		// position beyond end of range; bail out
 		if (s_next->hdr->ref_seq_start > fd->range.end) {
 		    fd->ooc = 1;
 		    cram_free_slice(s_next);
-		    s_next = NULL;
+		    c_next->slice = s_next = NULL;
 		    break;
 		}
 
 		// before start of range; skip to next slice
 		if (s_next->hdr->ref_seq_start + s_next->hdr->ref_seq_span-1 <
 		    fd->range.start) {
 		    cram_free_slice(s_next);
+		    c_next->slice = s_next = NULL;
 		    continue;
 		}
 	    }
@@ -3346,14 +3347,27 @@ int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam) {
  * Drains and frees the decode read-queue for a multi-threaded reader.
  */
 void cram_drain_rqueue(cram_fd *fd) {
+    cram_container *lc = NULL;
+
     if (!fd->pool)
 	return;
 
     // drain queue of any in-flight decode jobs
     while (!hts_tpool_process_empty(fd->rqueue)) {
 	hts_tpool_result *r = hts_tpool_next_result_wait(fd->rqueue);
 	cram_decode_job *j = (cram_decode_job *)hts_tpool_result_data(r);
-	cram_free_container(j->c);
+	if (j->c->slice == j->s)
+	    j->c->slice = NULL;
+	if (j->c != lc) {
+	    if (lc) {
+		if (fd->ctr == lc)
+		    fd->ctr = NULL;
+		if (fd->ctr_mt == lc)
+		    fd->ctr_mt = NULL;
+		cram_free_container(lc);
+	    }
+	    lc = j->c;
+	}
 	cram_free_slice(j->s);
 	hts_tpool_delete_result(r, 1);
     }
@@ -3362,9 +3376,28 @@ void cram_drain_rqueue(cram_fd *fd) {
     // due to the input queue being full.
     if (fd->job_pending) {
 	cram_decode_job *j = (cram_decode_job *)fd->job_pending;
-	cram_free_container(j->c);
+	if (j->c->slice == j->s)
+	    j->c->slice = NULL;
+	if (j->c != lc) {
+	    if (lc) {
+		if (fd->ctr == lc)
+		    fd->ctr = NULL;
+		if (fd->ctr_mt == lc)
+		    fd->ctr_mt = NULL;
+		cram_free_container(lc);
+	    }
+	    lc = j->c;
+	}
 	cram_free_slice(j->s);
 	free(j);
 	fd->job_pending = NULL;
     }
+
+    if (lc) {
+	if (fd->ctr == lc)
+	    fd->ctr = NULL;
+	if (fd->ctr_mt == lc)
+	    fd->ctr_mt = NULL;
+	cram_free_container(lc);
+    }
 }

cram/cram_index.c

@@ -497,6 +497,8 @@ int cram_seek_to_refpos(cram_fd *fd, cram_range *r) {
 
     if (fd->ctr) {
 	cram_free_container(fd->ctr);
+	if (fd->ctr_mt && fd->ctr_mt != fd->ctr)
+	    cram_free_container(fd->ctr_mt);
 	fd->ctr = NULL;
 	fd->ctr_mt = NULL;
 	fd->ooc = 0;

cram/cram_io.c

@@ -2746,6 +2746,7 @@ void cram_free_container(cram_container *c) {
     if (c->comp_hdr_block)
 	cram_free_block(c->comp_hdr_block);
 
+    // Free the slices; filled out by encoder only
     if (c->slices) {
         for (i = 0; i < c->max_slice; i++) {
             if (c->slices[i])
@@ -2756,8 +2757,10 @@ void cram_free_container(cram_container *c) {
         free(c->slices);
     }
 
+    // Free the current slice; set by both encoder & decoder
     if (c->slice) {
-        cram_free_slice(c->slice);
+	cram_free_slice(c->slice);
+	c->slice = NULL;
     }
 
     for (id = DS_RN; id < DS_TN; id++)
@@ -3136,7 +3139,7 @@ static int cram_flush_result(cram_fd *fd) {
 	    if (0 != cram_flush_container2(fd, c))
 		return -1;
 
-	/* Free the container */
+	// Free the slices; filled out by encoder only
 	if (c->slices) {
 	    for (i = 0; i < c->max_slice; i++) {
 		if (c->slices[i])
@@ -3147,6 +3150,7 @@ static int cram_flush_result(cram_fd *fd) {
 	    }
 	}
 
+	// Free the current slice; set by both encoder & decoder
 	if (c->slice) {
 	    cram_free_slice(c->slice);
 	    c->slice = NULL;