X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_import.c;h=da2bf942ed90573cb3c964b4ced593ba7cbcf3d8;hb=9f118264ea012adc21a46d7c03eaad4f9ce7d4d4;hp=29516c92ff42593313caf2833c38213d62ebdc52;hpb=80658e4d152b53bd55927c432ceece7702ab49d7;p=samtools.git

diff --git a/bam_import.c b/bam_import.c
index 29516c9..da2bf94 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -14,7 +14,7 @@
 #include "kseq.h"
 #include "khash.h"
 
-KSTREAM_INIT(gzFile, gzread, 8192)
+KSTREAM_INIT(gzFile, gzread, 16384)
 KHASH_MAP_INIT_STR(ref, uint64_t)
 
 void bam_init_header_hash(bam_header_t *header);
@@ -183,7 +183,7 @@ static inline void append_text(bam_header_t *header, kstring_t *str)
     // Sanity check
     if ( header->l_text+str->l+1 >= header->n_text )
     {
-        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,header->n_text,x,y);
+        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
         abort();
     }
 	strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
@@ -291,27 +291,32 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
 		z += str->l + 1;
 		if (str->s[0] != '*') {
+			uint32_t *cigar;
 			for (s = str->s; *s; ++s) {
-				if (isalpha(*s)) ++c->n_cigar;
+				if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;
 				else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
 			}
 			b->data = alloc_data(b, doff + c->n_cigar * 4);
+			cigar = bam1_cigar(b);
 			for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 				x = strtol(s, &t, 10);
 				op = toupper(*t);
-				if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
+				if (op == 'M') op = BAM_CMATCH;
 				else if (op == 'I') op = BAM_CINS;
 				else if (op == 'D') op = BAM_CDEL;
 				else if (op == 'N') op = BAM_CREF_SKIP;
 				else if (op == 'S') op = BAM_CSOFT_CLIP;
 				else if (op == 'H') op = BAM_CHARD_CLIP;
 				else if (op == 'P') op = BAM_CPAD;
+				else if (op == '=') op = BAM_CEQUAL;
+				else if (op == 'X') op = BAM_CDIFF;
+				else if (op == 'B') op = BAM_CBACK;
 				else parse_error(fp->n_lines, "invalid CIGAR operation");
 				s = t + 1;
-				bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
+				cigar[i] = bam_cigar_gen(x, op);
 			}
 			if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
-			c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+			c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar));
 			doff += c->n_cigar * 4;
 		} else {
 			if (!(c->flag&BAM_FUNMAP)) {
@@ -337,8 +342,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		z += str->l + 1;
 		if (strcmp(str->s, "*")) {
 			c->l_qseq = strlen(str->s);
-			if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
+			if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {
+				fprintf(stderr, "Line %ld, sequence length %i vs %i from CIGAR\n",
+						(long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
 				parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+			}
 			p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
 			memset(p, 0, (c->l_qseq+1)/2);
 			for (i = 0; i < c->l_qseq; ++i)
@@ -454,6 +462,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 	}
 	b->l_aux = doff - doff0;
 	b->data_len = doff;
+	if (bam_no_B) bam_remove_B(b);
 	return z;
 }