X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fbam_md.c;fp=samtools%2Fbam_md.c;h=0000000000000000000000000000000000000000;hp=17b0a4a4fa6943313be1b6d78b18c5255fe44982;hb=d02fe5283ed7a93a2f76a5d6dc6e37b40c11b9b1;hpb=d828f9c9aa78e3d1687265b52de841f3f3852089

diff --git a/samtools/bam_md.c b/samtools/bam_md.c
deleted file mode 100644
index 17b0a4a..0000000
--- a/samtools/bam_md.c
+++ /dev/null
@@ -1,175 +0,0 @@
-#include <unistd.h>
-#include <assert.h>
-#include <string.h>
-#include <ctype.h>
-#include "faidx.h"
-#include "sam.h"
-#include "kstring.h"
-
-void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
-{
-	uint8_t *seq = bam1_seq(b);
-	uint32_t *cigar = bam1_cigar(b);
-	bam1_core_t *c = &b->core;
-	int i, x, y, u = 0;
-	kstring_t *str;
-	uint8_t *old_md, *old_nm;
-	int32_t old_nm_i = -1, nm = 0;
-
-	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;
-		if (op == BAM_CMATCH) {
-			for (j = 0; j < l; ++j) {
-				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) { // 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; ++nm;
-				}
-			}
-			if (j < l) break;
-			x += l; y += l;
-		} else if (op == BAM_CDEL) {
-			ksprintf(str, "%d", u);
-			kputc('^', str);
-			for (j = 0; j < l; ++j) {
-				if (ref[x+j] == 0) break;
-				kputc(ref[x+j], str);
-			}
-			u = 0;
-			if (j < l) break;
-			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);
-	// apply max_nm
-	if (max_nm > 0 && nm >= max_nm) {
-		for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
-			int j, l = cigar[i]>>4, op = cigar[i]&0xf;
-			if (op == BAM_CMATCH) {
-				for (j = 0; j < l; ++j) {
-					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) { // a match
-						seq[z/2] |= (z&1)? 0x0f : 0xf0;
-						bam1_qual(b)[z] = 0;
-					}
-				}
-				if (j < l) break;
-				x += l; y += l;
-			} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
-			else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
-		}
-	}
-	// 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;
-		if (strlen((char*)old_md+1) == str->l) {
-			for (i = 0; i < str->l; ++i)
-				if (toupper(old_md[i+1]) != toupper(str->s[i]))
-					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);
-			bam_aux_del(b, old_md);
-			bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
-		}
-	}
-	free(str->s); free(str);
-}
-
-void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
-{
-	bam_fillmd1_core(b, ref, is_equal, 0);
-}
-
-int bam_fillmd(int argc, char *argv[])
-{
-	int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0;
-	samfile_t *fp, *fpout = 0;
-	faidx_t *fai;
-	char *ref = 0, mode_w[8], mode_r[8];
-	bam1_t *b;
-
-	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, "eubSn:")) >= 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;
-		case 'n': max_nm = atoi(optarg); 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, "\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;
-	}
-	fpout = samopen("-", mode_w, fp->header);
-	fai = fai_load(argv[optind+1]);
-
-	b = bam_init1();
-	while ((ret = samread(fp, b)) >= 0) {
-		if (b->core.tid >= 0) {
-			if (tid != b->core.tid) {
-				free(ref);
-				ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
-				tid = b->core.tid;
-				if (ref == 0)
-					fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
-							fp->header->target_name[tid]);
-			}
-			if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
-		}
-		samwrite(fpout, b);
-	}
-	bam_destroy1(b);
-
-	free(ref);
-	fai_destroy(fai);
-	samclose(fp); samclose(fpout);
-	return 0;
-}