X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam_view.c;h=06dd01a5ffa951dcb950a97681e7c5aca0b88971;hb=a7dfcd368cda94d5847d3f2b42d4288399d77835;hp=685784ddc95526626af4d7247aa734e986786b06;hpb=1ce5cbde83e25477ec59e08d5e14d6189065780b;p=samtools.git

diff --git a/sam_view.c b/sam_view.c
index 685784d..06dd01a 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -2,25 +2,45 @@
 #include <string.h>
 #include <stdio.h>
 #include <unistd.h>
+#include <math.h>
+#include "sam_header.h"
 #include "sam.h"
+#include "faidx.h"
 
 static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
 static char *g_library, *g_rg;
+static int g_sol2sanger_tbl[128];
+
+static void sol2sanger(bam1_t *b)
+{
+	int l;
+	uint8_t *qual = bam1_qual(b);
+	if (g_sol2sanger_tbl[30] == 0) {
+		for (l = 0; l != 128; ++l) {
+			g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499);
+			if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93;
+		}
+	}
+	for (l = 0; l < b->core.l_qseq; ++l) {
+		int q = qual[l];
+		if (q > 127) q = 127;
+		qual[l] = g_sol2sanger_tbl[q];
+	}
+}
 
 static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
 {
 	if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
 		return 1;
-	if (g_library || g_rg) {
+	if (g_rg) {
 		uint8_t *s = bam_aux_get(b, "RG");
-		if (s) {
-			if (g_rg && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
-			if (g_library) {
-				const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1));
-				return (p && strcmp(p, g_library) == 0)? 0 : 1;
-			} return 1;
-		} else return 1;
-	} else return 0;
+		if (s && strcmp(g_rg, (char*)(s + 1)) == 0) return 0;
+	}
+	if (g_library) {
+		const char *p = bam_get_library((bam_header_t*)h, b);
+		return (p && strcmp(p, g_library) == 0)? 0 : 1;
+	}
+	return 0;
 }
 
 // callback function for bam_fetch()
@@ -35,15 +55,16 @@ static int usage(int is_long_help);
 
 int main_samview(int argc, char *argv[])
 {
-	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
+	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, slx2sngr = 0;
 	int of_type = BAM_OFDEC, is_long_help = 0;
 	samfile_t *in = 0, *out = 0;
-	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
+	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
 
 	/* parse command-line options */
 	strcpy(in_mode, "r"); strcpy(out_mode, "w");
-	while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?")) >= 0) {
+	while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:C")) >= 0) {
 		switch (c) {
+		case 'C': slx2sngr = 1; break;
 		case 'S': is_bamin = 0; break;
 		case 'b': is_bamout = 1; break;
 		case 't': fn_list = strdup(optarg); is_bamin = 0; break;
@@ -59,6 +80,7 @@ int main_samview(int argc, char *argv[])
 		case 'x': of_type = BAM_OFHEX; break;
 		case 'X': of_type = BAM_OFSTR; break;
 		case '?': is_long_help = 1; break;
+		case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
 		default: return usage(is_long_help);
 		}
 	}
@@ -74,11 +96,17 @@ int main_samview(int argc, char *argv[])
 	if (is_uncompressed) strcat(out_mode, "u");
 	if (argc == optind) return usage(is_long_help);
 
+	// generate the fn_list if necessary
+	if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
 	// open file handlers
 	if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
 		fprintf(stderr, "[main_samview] fail to open file for reading.\n");
 		goto view_end;
 	}
+	if (in->header == 0) {
+		fprintf(stderr, "[main_samview] fail to read the header.\n");
+		goto view_end;
+	}
 	if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
 		fprintf(stderr, "[main_samview] fail to open file for writing.\n");
 		goto view_end;
@@ -88,9 +116,12 @@ int main_samview(int argc, char *argv[])
 	if (argc == optind + 1) { // convert/print the entire file
 		bam1_t *b = bam_init1();
 		int r;
-		while ((r = samread(in, b)) >= 0) // read one alignment from `in'
-			if (!__g_skip_aln(in->header, b))
+		while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
+			if (!__g_skip_aln(in->header, b)) {
+				if (slx2sngr) sol2sanger(b);
 				samwrite(out, b); // write the alignment to `out'
+			}
+		}
 		if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n");
 		bam_destroy1(b);
 	} else { // retrieve alignments in specified regions
@@ -116,7 +147,7 @@ int main_samview(int argc, char *argv[])
 
 view_end:
 	// close files, free and return
-	free(fn_list); free(fn_out); free(g_library); free(g_rg);
+	free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg);
 	samclose(in);
 	samclose(out);
 	return ret;
@@ -132,8 +163,9 @@ static int usage(int is_long_help)
 	fprintf(stderr, "         -S       input is SAM\n");
 	fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
 	fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
-	fprintf(stderr, "         -X       output FLAG in stirng (samtools-C specific)\n");
+	fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
 	fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
+	fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
 	fprintf(stderr, "         -o FILE  output file name [stdout]\n");
 	fprintf(stderr, "         -f INT   required flag, 0 for unset [0]\n");
 	fprintf(stderr, "         -F INT   filtering flag, 0 for unset [0]\n");
@@ -153,7 +185,7 @@ static int usage(int is_long_help)
      corresponding sequence length. The `.fai' file generated by `faidx'\n\
      can be used here. This file may be empty if reads are unaligned.\n\
 \n\
-  2. SAM->BAM conversion: `samtools view -bt ref.fa.fai in.sam.gz'.\n\
+  2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\
 \n\
   3. BAM->SAM conversion: `samtools view in.bam'.\n\
 \n\