X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=padding.c;h=d5fd15fb6a7cf49e782d506ebe74201748f9467e;hp=af3df94b57d6c0b33582559f9539532b3c435f1a;hb=8919a745585a68d671a1301b444e6edf7f4fdd4b;hpb=ededaf72960a46d036269b1aa7a5579df4798fd3

diff --git a/padding.c b/padding.c
index af3df94..d5fd15f 100644
--- a/padding.c
+++ b/padding.c
@@ -5,6 +5,7 @@
 #include "sam_header.h"
 #include "sam.h"
 #include "bam.h"
+#include "faidx.h"
 
 static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
 {
@@ -68,7 +69,52 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
 	assert(length == s->l);
 }
 
-int bam_pad2unpad(samfile_t *in, samfile_t *out)
+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;
+}
+
+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;
@@ -85,30 +131,46 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out)
 		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);
 				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)) 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[r.s[i]] : 45,
+							q.s[i] ? bam_nt16_rev_table[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));
 				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
+			} else if (fai) {
+				if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) 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);
@@ -185,6 +247,7 @@ static int usage(int is_long_help);
 int main_pad2unpad(int argc, char *argv[])
 {
 	samfile_t *in = 0, *out = 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;
@@ -215,34 +278,37 @@ int main_pad2unpad(int argc, char *argv[])
 	}
 
 	// Load FASTA reference (also needed for SAM -> BAM if missing header)
-	if (fn_ref) fn_list = samfaipath(fn_ref);
-
+	if (fn_ref) {
+		fn_list = samfaipath(fn_ref);
+		fai = fai_load(fn_ref);
+	}
 	// 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");
+		fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
 		ret = 1;
 		goto depad_end;
 	}
 
 	// Do the depad
-	ret = bam_pad2unpad(in, out);
+	ret = bam_pad2unpad(in, out, fai);
 
 depad_end:
 	// close files, free and return
 	free(fn_list); free(fn_out);
 	samclose(in);
 	samclose(out);
+	fai_destroy(fai);
 	return ret;
 }