X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=padding.c;h=a8da562d0872e8b0930bb2bdd3dcc9abb58bab7b;hp=9f8bca7e0fe13992aba557b176090936a34cb34a;hb=70c740facc966321754c6bfcc6d61ea056480638;hpb=dc39f05a341901dc9dd1ad0a8b6dad8b48c12967

diff --git a/padding.c b/padding.c
index 9f8bca7..a8da562 100644
--- a/padding.c
+++ b/padding.c
@@ -7,6 +7,8 @@
 #include "bam.h"
 #include "faidx.h"
 
+bam_header_t *bam_header_dup(const bam_header_t *h0); /*in sam.c*/
+
 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
 {
 	if (n != b->core.n_cigar) {
@@ -69,10 +71,88 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
 	assert(length == s->l);
 }
 
+int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
+{
+	char base;
+	char *fai_ref = 0;
+	int fai_ref_len = 0, k;
+
+	fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+	if (fai_ref_len != ref_len) {
+		fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len);
+		free(fai_ref);
+		return -1;
+	}
+	ks_resize(seq, ref_len);
+	seq->l = 0;
+	for (k = 0; k < ref_len; ++k) {
+		base = fai_ref[k];
+		if (base == '-' || base == '*') {
+			// Map gaps to null to match unpad_seq function
+			seq->s[seq->l++] = 0;
+		} else {
+			int i = bam_nt16_table[(int)base];
+			if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+				fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
+				free(fai_ref);
+				return -1;
+			}
+			seq->s[seq->l++] = i;
+		}
+	}
+	assert(ref_len == seq->l);
+	free(fai_ref);
+	return 0;
+}
+
+int get_unpadded_len(faidx_t *fai, char *ref_name, int padded_len)
+{
+	char base;
+	char *fai_ref = 0;
+	int fai_ref_len = 0, k;
+	int bases=0, gaps=0;
+
+	fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+	if (fai_ref_len != padded_len) {
+		fprintf(stderr, "[depad] ERROR: FASTA sequence '%s' length %i, expected %i\n", ref_name, fai_ref_len, padded_len);
+		free(fai_ref);
+		return -1;
+	}
+	for (k = 0; k < padded_len; ++k) {
+		//fprintf(stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref));
+		base = fai_ref[k];
+		if (base == '-' || base == '*') {
+			gaps += 1;
+		} else {
+			int i = bam_nt16_table[(int)base];
+			if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+				fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name);
+				free(fai_ref);
+				return -1;
+			}
+			bases += 1;
+		}
+	}
+	free(fai_ref);
+	assert (padded_len == bases + gaps);
+	return bases;
+}
+
+inline int * update_posmap(int *posmap, kstring_t ref)
+{
+	int i, k;
+	posmap = realloc(posmap, ref.m * sizeof(int));
+	for (i = k = 0; i < ref.l; ++i) {
+		posmap[i] = k;
+		if (ref.s[i]) ++k;
+	}
+	return posmap;
+}
+
 int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
 {
-	bam_header_t *h;
-	bam1_t *b;
+	bam_header_t *h = 0;
+	bam1_t *b = 0;
 	kstring_t r, q;
 	int r_tid = -1;
 	uint32_t *cigar2 = 0;
@@ -86,30 +166,53 @@ 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) {
-			int i, k;
-			/*
-			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) {
-				fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+				fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
 				return -1;
 			}
+			if (fai) {
+				// Check the embedded reference matches the FASTA file
+				if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) {
+					fprintf(stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", h->target_name[b->core.tid]);
+					return -1;
+				}
+				assert(r.l == q.l);
+				int i;
+				for (i = 0; i < r.l; ++i) {
+					if (r.s[i] != q.s[i]) {
+						// Show gaps as ASCII 45
+						fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+							h->target_name[b->core.tid], i+1,
+							r.s[i] ? bam_nt16_rev_table[(int)r.s[i]] : 45,
+							q.s[i] ? bam_nt16_rev_table[(int)q.s[i]] : 45);
+						return -1;
+					}
+				}
+			}
 			write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
 			replace_cigar(b, n2, cigar2);
-			posmap = realloc(posmap, r.m * sizeof(int));
-			for (i = k = 0; i < r.l; ++i) {
-				posmap[i] = k;
-				if (r.s[i]) ++k;
-			}
+			posmap = update_posmap(posmap, r);
 		} else if (b->core.n_cigar > 0) {
 			int i, k, op;
 			if (b->core.tid < 0) {
-				fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
+				fprintf(stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam1_qname(b));
 				return -1;
-			} else if (b->core.tid != r_tid) {
-				fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
+			} 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]);
+					return -1;
+				}
+				posmap = update_posmap(posmap, r);
+				r_tid = b->core.tid;
+				// fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
+			} else {				
+				fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
 				return -1;
 			}
 			unpad_seq(b, &q);
@@ -169,6 +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);
 	}
@@ -181,12 +316,70 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
 	return ret;
 }
 
+bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
+{
+	int i = 0, unpadded_len = 0;
+	bam_header_t *header = 0 ;
+
+	header = bam_header_dup(old);
+	for (i = 0; i < old->n_targets; ++i) {
+		unpadded_len = get_unpadded_len(fai, old->target_name[i], old->target_len[i]);
+		if (unpadded_len < 0) {
+			fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]);
+		} else {
+			header->target_len[i] = unpadded_len;
+			//fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
+		}
+	}
+	/* Duplicating the header allocated new buffer for header string */
+	/* After modifying the @SQ lines it will only get smaller, since */
+	/* the LN entries will be the same or shorter, and we'll remove */
+	/* any MD entries (MD5 checksums). */
+	assert(strlen(old->text) == strlen(header->text));
+	assert (0==strcmp(old->text, header->text));
+	const char *text;
+	text = old->text;
+	header->text[0] = '\0'; /* Resuse the allocated buffer */
+	char * newtext = header->text;
+	char * end=NULL;
+	while (text[0]=='@') {
+		end = strchr(text, '\n');
+		assert(end != 0);
+		if (text[1]=='S' && text[2]=='Q' && text[3]=='\t') {
+			/* TODO - edit the @SQ line here to remove MD and fix LN. */
+			/* For now just remove the @SQ line, and samtools will */
+			/* automatically generate a minimal replacement with LN. */
+			/* However, that discards any other tags like AS, SP, UR. */
+			//fprintf(stderr, "[depad] Removing @SQ line\n");
+		} else {
+			/* Copy this line to the new header */
+			strncat(newtext, text, end - text + 1);
+		}
+		text = end + 1;
+	}
+	assert (text[0]=='\0');
+	/* Check we didn't overflow the buffer */
+	assert (strlen(header->text) <= strlen(old->text));
+	if (strlen(header->text) < header->l_text) {
+		//fprintf(stderr, "[depad] Reallocating header buffer\n");
+		assert (newtext == header->text);
+		newtext = malloc(strlen(header->text) + 1);
+		strcpy(newtext, header->text);
+		free(header->text);
+		header->text = newtext;
+		header->l_text = strlen(newtext);
+	}
+	//fprintf(stderr, "[depad] Here is the new header (pending @SQ lines),\n\n%s\n(end)\n", header->text);
+	return header;
+}
+
 static int usage(int is_long_help);
 
 int main_pad2unpad(int argc, char *argv[])
 {
 	samfile_t *in = 0, *out = 0;
-	faidx_t *fai;
+        bam_header_t *h = 0;
+	faidx_t *fai = 0;
 	int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
 	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
         int ret=0;
@@ -200,7 +393,7 @@ int main_pad2unpad(int argc, char *argv[])
 		case 'o': fn_out = strdup(optarg); break;
 		case 'u': assert(is_bamout == 1); compress_level = 0; break;
 		case '1': assert(is_bamout == 1); compress_level = 1; break;
-		case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
+		case 'T': fn_ref = strdup(optarg); break;
                 case '?': is_long_help = 1; break;
 		default: return usage(is_long_help);
 		}
@@ -223,18 +416,28 @@ int main_pad2unpad(int argc, char *argv[])
 	}
 	// open file handlers
 	if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
-		fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
+		fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
 		ret = 1;
 		goto depad_end;
 	}
 	if (in->header == 0) {
-		fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]);
+		fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
 		ret = 1;
 		goto depad_end;
 	}
-	/* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
-	if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
-		fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+	if (in->header->text == 0 || in->header->l_text == 0) {
+		fprintf(stderr, "[depad] Warning - failed to read any header text from \"%s\".\n", argv[optind]);
+		assert (0 == in->header->l_text);
+		assert (0 == in->header->text);
+	}
+	if (fn_ref) {
+		h = fix_header(in->header, fai);
+	} else {
+		fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
+		h = in->header;
+	}
+	if ((out = samopen(fn_out? fn_out : "-", out_mode, h)) == 0) {
+		fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
 		ret = 1;
 		goto depad_end;
 	}
@@ -244,10 +447,11 @@ int main_pad2unpad(int argc, char *argv[])
 
 depad_end:
 	// close files, free and return
-	free(fn_list); free(fn_out);
+	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;
 }