X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_md.c;h=8d074870d336677cee2e606ab05ee81a2b4a6f1e;hp=a20f9b354d477c1f11a8d98854ff9ec7682d01c1;hb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/bam_md.c b/bam_md.c
index a20f9b3..8d07487 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -3,7 +3,7 @@
 #include <string.h>
 #include <ctype.h>
 #include "faidx.h"
-#include "bam.h"
+#include "sam.h"
 #include "kstring.h"
 
 void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
@@ -13,11 +13,9 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 	bam1_core_t *c = &b->core;
 	int i, x, y, u = 0;
 	kstring_t *str;
-	uint8_t *old_md;
+	uint8_t *old_md, *old_nm;
+	int32_t old_nm_i = -1, nm = 0;
 
-	old_md = bam_aux_get(b, "MD");
-	if (c->flag & BAM_FUNMAP) return;
-	if (old_md && !is_equal) return; // no need to add MD
 	str = (kstring_t*)calloc(1, sizeof(kstring_t));
 	for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
 		int j, l = cigar[i]>>4, op = cigar[i]&0xf;
@@ -26,13 +24,13 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 				int z = y + j;
 				int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
 				if (ref[x+j] == 0) break; // out of boundary
-				if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) {
+				if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
 					if (is_equal) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
 					++u;
 				} else {
 					ksprintf(str, "%d", u);
 					kputc(ref[x+j], str);
-					u = 0;
+					u = 0; ++nm;
 				}
 			}
 			if (j < l) break;
@@ -46,14 +44,27 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 			}
 			u = 0;
 			if (j < l) break;
-			x += l;
+			x += l; nm += l;
 		} else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
 			y += l;
+			if (op == BAM_CINS) nm += l;
 		} else if (op == BAM_CREF_SKIP) {
 			x += l;
 		}
 	}
 	ksprintf(str, "%d", u);
+	// update NM
+	old_nm = bam_aux_get(b, "NM");
+	if (c->flag & BAM_FUNMAP) return;
+	if (old_nm) old_nm_i = bam_aux2i(old_nm);
+	if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
+	else if (nm != old_nm_i) {
+		fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
+		bam_aux_del(b, old_nm);
+		bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
+	}
+	// update MD
+	old_md = bam_aux_get(b, "MD");
 	if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
 	else {
 		int is_diff = 0;
@@ -63,55 +74,73 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 					break;
 			if (i < str->l) is_diff = 1;
 		} else is_diff = 1;
-		if (is_diff)
-			fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' != '%s'\n", bam1_qname(b), old_md+1, str->s);
+		if (is_diff) {
+			fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
+			bam_aux_del(b, old_md);
+			bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
+		}
 	}
 	free(str->s); free(str);
 }
 
 int bam_fillmd(int argc, char *argv[])
 {
-	int c, is_equal = 0, tid = -2, ret, len;
-	bamFile fp, fpout = 0;
-	bam_header_t *header;
+	int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed;
+	samfile_t *fp, *fpout = 0;
 	faidx_t *fai;
-	char *ref = 0;
+	char *ref = 0, mode_w[8], mode_r[8];
 	bam1_t *b;
 
-	while ((c = getopt(argc, argv, "e")) >= 0) {
+	is_bam_out = is_sam_in = is_uncompressed = 0;
+	mode_w[0] = mode_r[0] = 0;
+	strcpy(mode_r, "r"); strcpy(mode_w, "w");
+	while ((c = getopt(argc, argv, "eubS")) >= 0) {
 		switch (c) {
 		case 'e': is_equal = 1; break;
+		case 'b': is_bam_out = 1; break;
+		case 'u': is_uncompressed = is_bam_out = 1; break;
+		case 'S': is_sam_in = 1; break;
 		default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
 		}
 	}
+	if (!is_sam_in) strcat(mode_r, "b");
+	if (is_bam_out) strcat(mode_w, "b");
+	else strcat(mode_w, "h");
+	if (is_uncompressed) strcat(mode_w, "u");
 	if (optind + 1 >= argc) {
-		fprintf(stderr, "Usage: bam fillmd [-e] <aln.bam> <ref.fasta>\n");
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   samtools fillmd [-eubS] <aln.bam> <ref.fasta>\n\n");
+		fprintf(stderr, "Options: -e       change identical bases to '='\n");
+		fprintf(stderr, "         -u       uncompressed BAM output (for piping)\n");
+		fprintf(stderr, "         -b       compressed BAM output\n");
+		fprintf(stderr, "         -S       the input is SAM with header\n\n");
+		return 1;
+	}
+	fp = samopen(argv[optind], mode_r, 0);
+	if (fp == 0) return 1;
+	if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) {
+		fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
 		return 1;
 	}
-	fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
-	assert(fp);
-	header = bam_header_read(fp);
-	fpout = bam_dopen(fileno(stdout), "w");
-	bam_header_write(fpout, header);
+	fpout = samopen("-", mode_w, fp->header);
 	fai = fai_load(argv[optind+1]);
 
 	b = bam_init1();
-	while ((ret = bam_read1(fp, b)) >= 0) {
+	while ((ret = samread(fp, b)) >= 0) {
 		if (b->core.tid >= 0) {
 			if (tid != b->core.tid) {
 				free(ref);
-				ref = fai_fetch(fai, header->target_name[b->core.tid], &len);
+				ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
 				tid = b->core.tid;
 			}
 			bam_fillmd1(b, ref, is_equal);
 		}
-		bam_write1(fpout, b);
+		samwrite(fpout, b);
 	}
 	bam_destroy1(b);
 
 	free(ref);
 	fai_destroy(fai);
-	bam_header_destroy(header);
-	bam_close(fp); bam_close(fpout);
+	samclose(fp); samclose(fpout);
 	return 0;
 }