X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_tview.c;h=f8a1f2c3c1eeeef25542316d37af98f9819903fa;hb=70c740facc966321754c6bfcc6d61ea056480638;hp=4eea955ce05574051c60591dac6a44b5a1ad5edc;hpb=c350a570e955d5b4c2c13f607b7442df6d332c67;p=samtools.git

diff --git a/bam_tview.c b/bam_tview.c
index 4eea955..f8a1f2c 100644
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -20,9 +20,14 @@
 #include <assert.h>
 #include <string.h>
 #include <math.h>
+#include <unistd.h>
 #include "bam.h"
 #include "faidx.h"
 #include "bam2bcf.h"
+#include "sam_header.h"
+#include "khash.h"
+
+KHASH_MAP_INIT_STR(kh_rg, const char *)
 
 char bam_aux_getCEi(bam1_t *b, int i);
 char bam_aux_getCSi(bam1_t *b, int i);
@@ -55,6 +60,7 @@ typedef struct {
 
 	int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
 	char *ref;
+    khash_t(kh_rg) *rg_hash;
 } tview_t;
 
 int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
@@ -114,7 +120,6 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 				if (!p->is_del) {
 					if (tv->base_for == TV_BASE_COLOR_SPACE && 
 							(c = bam_aux_getCSi(p->b, p->qpos))) {
-						c = bam_aux_getCSi(p->b, p->qpos);
 						// assume that if we found one color, we will be able to get the color error
 						if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
 					} else {
@@ -196,7 +201,7 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 	return 0;
 }
 
-tview_t *tv_init(const char *fn, const char *fn_fa)
+tview_t *tv_init(const char *fn, const char *fn_fa, char *samples)
 {
 	tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
 	tv->is_dot = 1;
@@ -211,6 +216,32 @@ tview_t *tv_init(const char *fn, const char *fn_fa)
 	tv->bca = bcf_call_init(0.83, 13);
 	tv->ins = 1;
 
+    if ( samples ) 
+    {
+        if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text);
+        void *iter = tv->header->dict;
+        const char *key, *val;
+        int n = 0;
+        tv->rg_hash = kh_init(kh_rg);
+        while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) )
+        {
+            if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) )
+            {
+                khiter_t k = kh_get(kh_rg, tv->rg_hash, key);
+                if ( k != kh_end(tv->rg_hash) ) continue;
+                int ret;
+                k = kh_put(kh_rg, tv->rg_hash, key, &ret);
+                kh_value(tv->rg_hash, k) = val;
+                n++;
+            }
+        }
+        if ( !n )
+        {
+            fprintf(stderr,"The sample or read group \"%s\" not present.\n", samples);
+            exit(-1);
+        }
+    }
+
 	initscr();
 	keypad(stdscr, TRUE);
 	clear();
@@ -252,6 +283,13 @@ void tv_destroy(tview_t *tv)
 int tv_fetch_func(const bam1_t *b, void *data)
 {
 	tview_t *tv = (tview_t*)data;
+    if ( tv->rg_hash )
+    {
+        const uint8_t *rg = bam_aux_get(b, "RG");
+        if ( !rg ) return 0; 
+        khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
+        if ( k == kh_end(tv->rg_hash) ) return 0;
+    }
 	if (tv->no_skip) {
 		uint32_t *cigar = bam1_cigar(b); // this is cheating...
 		int i;
@@ -304,7 +342,7 @@ static void tv_win_goto(tview_t *tv, int *tid, int *pos)
 		int c = wgetch(tv->wgoto);
 		wrefresh(tv->wgoto);
 		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
-			--l;
+			if(l > 0) --l;
 		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
 			int _tid = -1, _beg, _end;
 			if (str[0] == '=') {
@@ -416,15 +454,49 @@ end_loop:
 	return;
 }
 
+void error(const char *format, ...)
+{
+    if ( !format )
+    {
+        fprintf(stderr, "\n");
+        fprintf(stderr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
+        fprintf(stderr, "Options:\n");
+        fprintf(stderr, "   -p chr:pos      go directly to this position\n");
+        fprintf(stderr, "   -s STR          display only reads from this sample or grou\n");
+        fprintf(stderr, "\n\n");
+    }
+    else
+    {
+        va_list ap;
+        va_start(ap, format);
+        vfprintf(stderr, format, ap);
+        va_end(ap);
+    }
+    exit(-1);
+}
+
+
 int bam_tview_main(int argc, char *argv[])
 {
 	tview_t *tv;
-	if (argc == 1) {
-		fprintf(stderr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
-		return 1;
-	}
-	tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
-	tv_draw_aln(tv, 0, 0);
+    char *samples=NULL, *position=NULL;
+    int c;
+    while ((c = getopt(argc, argv, "s:p:")) >= 0) {
+        switch (c) {
+            case 's': samples=optarg; break;
+            case 'p': position=optarg; break;
+            default: error(NULL);
+        }
+    }
+	if (argc==optind) error(NULL);
+	tv = tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+    if ( position )
+    {
+        int _tid = -1, _beg, _end;
+        bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
+        if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
+    }
+	tv_draw_aln(tv, tv->curr_tid, tv->left_pos);
 	tv_loop(tv);
 	tv_destroy(tv);
 	return 0;