Merge remote branch 'remotes/pd3/master'

Conflicts:
	misc/bamcheck.c

diff --git a/bam.h b/bam.h
index 159f7159cb2006e75a48de5810485c46b609e832..a3305e3cf4b758edaaeaf201ea4fbc87ab8f919b 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -40,7 +40,7 @@
   @copyright Genome Research Ltd.
  */
 
-#define BAM_VERSION "0.1.18-r579"
+#define BAM_VERSION "0.1.18-r580"
 
 #include <stdint.h>
 #include <stdlib.h>
@@ -773,7 +773,7 @@ static inline int bam_aux_type2size(int x)
 {
        if (x == 'C' || x == 'c' || x == 'A') return 1;
        else if (x == 'S' || x == 's') return 2;
-       else if (x == 'I' || x == 'i' || x == 'f') return 4;
+       else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4;
        else return 0;
 }
 

diff --git a/misc/plot-bamcheck b/misc/plot-bamcheck
index e5f5b4aba135ffed6785c600f2a57581f1a2e44f..1792c6ffe8c0647b640a075f301f6e6cd7293c5d 100755 (executable)
--- a/misc/plot-bamcheck
+++ b/misc/plot-bamcheck
@@ -663,7 +663,8 @@ sub plot_coverage
 
     my @vals;
     for my $cov (@{$$opts{dat}{COV}}) { push @vals,$$cov[2]; }
-    my $p99 = percentile(99.8,@vals);
+    my $i = percentile(99.8,@vals);
+    my $p99 = $$opts{dat}{COV}[$i][1];
 
     my $args = get_defaults($opts,"$$opts{prefix}coverage.png");
     my $fh = $$args{fh};

diff --git a/padding.c b/padding.c
index 88945e2ca5c54c1a592a45899358996ddd810ece..a8da562d0872e8b0930bb2bdd3dcc9abb58bab7b 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -166,7 +166,7 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                uint32_t *cigar = bam1_cigar(b);
                n2 = 0;
                if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
-                       // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
+                       // fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam1_qname(b));
                        r_tid = b->core.tid;
                        unpad_seq(b, &r);
                        if (h->target_len[r_tid] != r.l) {
@@ -202,6 +202,7 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                                return -1;
                        } else if (b->core.tid == r_tid) {
                                ; // good case, reference available
+                               //fprintf(stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam1_qname(b));
                        } else if (fai) {
                                if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
                                        fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
@@ -271,6 +272,38 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                        n2 = k;
                        replace_cigar(b, n2, cigar2);
                        b->core.pos = posmap[b->core.pos];
+                       if (b->core.mtid < 0 || b->core.mpos < 0) {
+                               /* Nice case, no mate to worry about*/
+                               // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
+                               /* TODO - Warning if FLAG says mate should be mapped? */
+                               /* Clean up funny input where mate position is given but mate reference is missing: */
+                               b->core.mtid = -1;
+                               b->core.mpos = -1;
+                       } else if (b->core.mtid == b->core.tid) {
+                               /* Nice case, same reference */
+                               // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
+                               b->core.mpos = posmap[b->core.mpos];
+                       } else {
+                               /* Nasty case, Must load alternative posmap */
+                               // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+                               if (!fai) {
+                                       fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]);
+                                       return -1;
+                               }
+                               /* Temporarily load the other reference sequence */
+                               if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) {
+                                       fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]);
+                                       return -1;
+                               }
+                               posmap = update_posmap(posmap, r);
+                               b->core.mpos = posmap[b->core.mpos];
+                               /* Restore the reference and posmap*/
+                               if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
+                                       fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
+                                       return -1;
+                               }
+                               posmap = update_posmap(posmap, r);
+                       }
                }
                samwrite(out, b);
        }
@@ -330,7 +363,7 @@ bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
        if (strlen(header->text) < header->l_text) {
                //fprintf(stderr, "[depad] Reallocating header buffer\n");
                assert (newtext == header->text);
-               newtext = calloc(strlen(header->text) + 1, 1);
+               newtext = malloc(strlen(header->text) + 1);
                strcpy(newtext, header->text);
                free(header->text);
                header->text = newtext;
@@ -414,11 +447,11 @@ int main_pad2unpad(int argc, char *argv[])
 
 depad_end:
        // close files, free and return
-       free(fn_list); free(fn_out);
-        if (h != in->header) bam_header_destroy(h);
+       if (fai) fai_destroy(fai);
+       if (h != in->header) bam_header_destroy(h);
        samclose(in);
        samclose(out);
-       fai_destroy(fai);
+       free(fn_list); free(fn_out);
        return ret;
 }