From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 12 Mar 2013 13:25:17 +0000 (+0000)
Subject: Merge remote branch 'remotes/master/master' into fb-annots
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=60e0a8467ddbd0b89f15d201dcfe10c8796552b2;hp=6842e4470dcbd381d0893690b7d07344fd08e831

Merge remote branch 'remotes/master/master' into fb-annots
---

diff --git a/Makefile b/Makefile
index dbd90af..2f51bfc 100644
--- a/Makefile
+++ b/Makefile
@@ -9,7 +9,8 @@ LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
 AOBJS=		bam_tview.o bam_plcmd.o sam_view.o \
 			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
 			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
-			cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o
+			cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
+			bam_tview_curses.o bam_tview_html.o
 PROG=		samtools
 INCLUDES=	-I.
 SUBDIRS=	. bcftools misc
@@ -46,10 +47,10 @@ samtools:lib-recur $(AOBJS)
 		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
 
 razip:razip.o razf.o $(KNETFILE_O)
-		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
+		$(CC) $(CFLAGS) -o $@ $^ -lz
 
 bgzip:bgzip.o bgzf.o $(KNETFILE_O)
-		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz -lpthread
+		$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
 
 bgzf.o:bgzf.c bgzf.h
 		$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
@@ -62,7 +63,9 @@ bam_pileup.o:bam.h razf.h ksort.h
 bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
 bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
 bam_lpileup.o:bam.h ksort.h
-bam_tview.o:bam.h faidx.h
+bam_tview.o:bam.h faidx.h bam_tview.h
+bam_tview_curses.o:bam.h faidx.h bam_tview.h
+bam_tview_html.o:bam.h faidx.h bam_tview.h
 bam_sort.o:bam.h ksort.h razf.h
 bam_md.o:bam.h faidx.h
 sam_header.o:sam_header.h khash.h
diff --git a/bam2depth.c b/bam2depth.c
index 87a4c5b..02311ef 100644
--- a/bam2depth.c
+++ b/bam2depth.c
@@ -32,37 +32,58 @@ static int read_bam(void *data, bam1_t *b) // read level filters better go here
 	return ret;
 }
 
+int read_file_list(const char *file_list,int *n,char **argv[]);
+
 #ifdef _MAIN_BAM2DEPTH
 int main(int argc, char *argv[])
 #else
 int main_depth(int argc, char *argv[])
 #endif
 {
-	int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0;
+	int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0, nfiles;
 	const bam_pileup1_t **plp;
 	char *reg = 0; // specified region
 	void *bed = 0; // BED data structure
+    char *file_list = NULL, **fn = NULL;
 	bam_header_t *h = 0; // BAM header of the 1st input
 	aux_t **data;
 	bam_mplp_t mplp;
 
 	// parse the command line
-	while ((n = getopt(argc, argv, "r:b:q:Q:l:")) >= 0) {
+	while ((n = getopt(argc, argv, "r:b:q:Q:l:f:")) >= 0) {
 		switch (n) {
 			case 'l': min_len = atoi(optarg); break; // minimum query length
 			case 'r': reg = strdup(optarg); break;   // parsing a region requires a BAM header
 			case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
 			case 'q': baseQ = atoi(optarg); break;   // base quality threshold
 			case 'Q': mapQ = atoi(optarg); break;    // mapping quality threshold
+			case 'f': file_list = optarg; break;
 		}
 	}
-	if (optind == argc) {
-		fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-l minQLen] [-b in.bed] <in1.bam> [...]\n");
+	if (optind == argc && !file_list) {
+        fprintf(stderr, "\n");
+        fprintf(stderr, "Usage: samtools depth [options] in1.bam [in2.bam [...]]\n");
+        fprintf(stderr, "Options:\n");
+        fprintf(stderr, "   -b <bed>            list of positions or regions\n");
+        fprintf(stderr, "   -f <list>           list of input BAM filenames, one per line [null]\n");
+        fprintf(stderr, "   -l <int>            minQLen\n");
+        fprintf(stderr, "   -q <int>            base quality threshold\n");
+        fprintf(stderr, "   -Q <int>            mapping quality threshold\n");
+        fprintf(stderr, "   -r <chr:from-to>    region\n");
+        fprintf(stderr, "\n");
 		return 1;
 	}
 
 	// initialize the auxiliary data structures
-	n = argc - optind; // the number of BAMs on the command line
+    if (file_list) 
+    {
+        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+        n = nfiles;
+        argv = fn;
+        optind = 0;
+    }
+    else
+        n = argc - optind; // the number of BAMs on the command line
 	data = calloc(n, sizeof(void*)); // data[i] for the i-th input
 	beg = 0; end = 1<<30; tid = -1;  // set the default region
 	for (i = 0; i < n; ++i) {
@@ -113,5 +134,10 @@ int main_depth(int argc, char *argv[])
 	}
 	free(data); free(reg);
 	if (bed) bed_destroy(bed);
+    if ( file_list )
+    {
+        for (i=0; i<n; i++) free(fn[i]);
+        free(fn);
+    }
 	return 0;
 }
diff --git a/bam_aux.c b/bam_aux.c
index 28b22e3..4bbf975 100644
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -141,6 +141,10 @@ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *be
 			} else s[name_end] = ':', name_end = l;
 		}
 	} else iter = kh_get(s, h, str);
+        if (iter == kh_end(h)) {
+          free(s); 
+          return -1;
+        }
 	*ref_id = kh_val(h, iter);
 	// parse the interval
 	if (name_end < l) {
diff --git a/bam_index.c b/bam_index.c
index d6b94e2..f916e04 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -464,6 +464,7 @@ bam_index_t *bam_index_load(const char *fn)
 		strcat(strcpy(fnidx, fn), ".bai");
 		fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
 		download_from_remote(fnidx);
+        free(fnidx);
 		idx = bam_index_load_local(fn);
 	}
 	if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
@@ -494,6 +495,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
 	if (fpidx == 0) {
 		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
 		free(fnidx);
+        bam_index_destroy(idx);
 		return -1;
 	}
 	bam_index_save(idx, fpidx);
diff --git a/bam_plcmd.c b/bam_plcmd.c
index e45c8c8..9c4f273 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -4,6 +4,8 @@
 #include <ctype.h>
 #include <string.h>
 #include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
 #include "sam.h"
 #include "faidx.h"
 #include "kstring.h"
@@ -80,6 +82,7 @@ int bed_overlap(const void *_h, const char *chr, int beg, int end);
 
 typedef struct {
 	int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
+    int rflag_require, rflag_filter;
 	int openQ, extQ, tandemQ, min_support; // for indels
 	double min_frac; // for indels
 	char *reg, *pl_list;
@@ -117,6 +120,8 @@ static int mplp_func(void *data, bam1_t *b)
 			skip = 1;
 			continue;
 		}
+        if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
 		if (ma->conf->bed) { // test overlap
 			skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
 			if (skip) continue;
@@ -397,11 +402,15 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 }
 
 #define MAX_PATH_LEN 1024
-static int read_file_list(const char *file_list,int *n,char **argv[])
+int read_file_list(const char *file_list,int *n,char **argv[])
 {
     char buf[MAX_PATH_LEN];
-    int len, nfiles;
-    char **files;
+    int len, nfiles = 0;
+    char **files = NULL;
+    struct stat sb;
+
+    *n = 0;
+    *argv = NULL;
 
     FILE *fh = fopen(file_list,"r");
     if ( !fh )
@@ -410,28 +419,33 @@ static int read_file_list(const char *file_list,int *n,char **argv[])
         return 1;
     }
 
-    // Speed is not an issue here, determine the number of files by reading the file twice
-    nfiles = 0;
-    while ( fgets(buf,MAX_PATH_LEN,fh) ) nfiles++;
-
-    if ( fseek(fh, 0L, SEEK_SET) )
-    {
-        fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
-        return 1;
-    }
-
     files = calloc(nfiles,sizeof(char*));
     nfiles = 0;
     while ( fgets(buf,MAX_PATH_LEN,fh) ) 
     {
+        // allow empty lines and trailing spaces
         len = strlen(buf);
         while ( len>0 && isspace(buf[len-1]) ) len--;
         if ( !len ) continue;
 
-        files[nfiles] = malloc(sizeof(char)*(len+1)); 
-        strncpy(files[nfiles],buf,len);
-        files[nfiles][len] = 0;
+        // check sanity of the file list
+        buf[len] = 0;
+        if (stat(buf, &sb) != 0)
+        {
+            // no such file, check if it is safe to print its name
+            int i, safe_to_print = 1;
+            for (i=0; i<len; i++)
+                if (!isprint(buf[i])) { safe_to_print = 0; break; } 
+            if ( safe_to_print )
+                fprintf(stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+            else
+                fprintf(stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+            return 1;
+        }
+
         nfiles++;
+        files = realloc(files,nfiles*sizeof(char*));
+        files[nfiles-1] = strdup(buf);
     }
     fclose(fh);
     if ( !nfiles )
@@ -460,8 +474,16 @@ int bam_mpileup(int argc, char *argv[])
 	mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
 	mplp.min_frac = 0.002; mplp.min_support = 1;
 	mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
-	while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV")) >= 0) {
+    static struct option lopts[] = 
+    {
+        {"rf",1,0,1},   // require flag
+        {"ff",1,0,2},   // filter flag
+        {0,0,0,0}
+    };
+	while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
 		switch (c) {
+        case  1 : mplp.rflag_require = strtol(optarg,0,0); break;
+        case  2 : mplp.rflag_filter  = strtol(optarg,0,0); break;
 		case 'f':
 			mplp.fai = fai_load(optarg);
 			if (mplp.fai == 0) return 1;
@@ -517,7 +539,7 @@ int bam_mpileup(int argc, char *argv[])
 		fprintf(stderr, "       -6           assume the quality is in the Illumina-1.3+ encoding\n");
 		fprintf(stderr, "       -A           count anomalous read pairs\n");
 		fprintf(stderr, "       -B           disable BAQ computation\n");
-		fprintf(stderr, "       -b FILE      list of input BAM files [null]\n");
+		fprintf(stderr, "       -b FILE      list of input BAM filenames, one per line [null]\n");
 		fprintf(stderr, "       -C INT       parameter for adjusting mapQ; 0 to disable [0]\n");
 		fprintf(stderr, "       -d INT       max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
 		fprintf(stderr, "       -E           recalculate extended BAQ on the fly thus ignoring existing BQs\n");
@@ -529,6 +551,8 @@ int bam_mpileup(int argc, char *argv[])
 		fprintf(stderr, "       -R           ignore RG tags\n");
 		fprintf(stderr, "       -q INT       skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
 		fprintf(stderr, "       -Q INT       skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+		fprintf(stderr, "       --rf INT     required flags: skip reads with mask bits unset []\n");
+		fprintf(stderr, "       --ff INT     filter flags: skip reads with mask bits set []\n");
 		fprintf(stderr, "\nOutput options:\n\n");
 		fprintf(stderr, "       -D           output per-sample DP in BCF (require -g/-u)\n");
 		fprintf(stderr, "       -g           generate BCF output (genotype likelihoods)\n");
diff --git a/bam_sort.c b/bam_sort.c
index 7d00cd1..c46bce3 100644
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -434,12 +434,13 @@ static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, c
   @param  prefix   prefix of the output and the temporary files; upon
 	                   sucessess, prefix.bam will be written.
   @param  max_mem  approxiate maximum memory (very inaccurate)
+  @param full_path the given output path is the full path and not just the prefix
 
   @discussion It may create multiple temporary subalignment files
   and then merge them by calling bam_merge_core(). This function is
   NOT thread safe.
  */
-void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level)
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level, int full_path)
 {
 	int ret, i, n_files = 0;
 	size_t mem, max_k, k, max_mem;
@@ -447,6 +448,8 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 	bamFile fp;
 	bam1_t *b, **buf;
 	char *fnout = 0;
+	char const *suffix = ".bam";
+	if (full_path) suffix += 4;
 
 	if (n_threads < 2) n_threads = 1;
 	g_is_by_qname = is_by_qname;
@@ -489,7 +492,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 	// output file name
 	fnout = calloc(strlen(prefix) + 20, 1);
 	if (is_stdout) sprintf(fnout, "-");
-	else sprintf(fnout, "%s.bam", prefix);
+	else sprintf(fnout, "%s%s", prefix, suffix);
 	// write the final output
 	if (n_files == 0) { // a single block
 		char mode[8];
@@ -504,7 +507,7 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 		fns = (char**)calloc(n_files, sizeof(char*));
 		for (i = 0; i < n_files; ++i) {
 			fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
-			sprintf(fns[i], "%s.%.4d.bam", prefix, i);
+			sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix);
 		}
 		bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);
 		for (i = 0; i < n_files; ++i) {
@@ -527,15 +530,16 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
 
 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
 {
-	bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1);
+	bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 0);
 }
 
 int bam_sort(int argc, char *argv[])
 {
 	size_t max_mem = 768<<20; // 512MB
-	int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1;
-	while ((c = getopt(argc, argv, "nom:@:l:")) >= 0) {
+	int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0;
+	while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) {
 		switch (c) {
+		case 'f': full_path = 1; break;
 		case 'o': is_stdout = 1; break;
 		case 'n': is_by_qname = 1; break;
 		case 'm': {
@@ -554,6 +558,7 @@ int bam_sort(int argc, char *argv[])
 		fprintf(stderr, "\n");
 		fprintf(stderr, "Usage:   samtools sort [options] <in.bam> <out.prefix>\n\n");
 		fprintf(stderr, "Options: -n        sort by read name\n");
+		fprintf(stderr, "         -f        use <out.prefix> as full file name instead of prefix\n");
 		fprintf(stderr, "         -o        final output to stdout\n");
 		fprintf(stderr, "         -l INT    compression level, from 0 to 9 [-1]\n");
 		fprintf(stderr, "         -@ INT    number of sorting and compression threads [1]\n");
@@ -561,6 +566,6 @@ int bam_sort(int argc, char *argv[])
 		fprintf(stderr, "\n");
 		return 1;
 	}
-	bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level);
+	bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level, full_path);
 	return 0;
 }
diff --git a/bam_tview.c b/bam_tview.c
index f8a1f2c..06d5e33 100644
--- a/bam_tview.c
+++ b/bam_tview.c
@@ -1,67 +1,81 @@
-#undef _HAVE_CURSES
-
-#if _CURSES_LIB == 0
-#elif _CURSES_LIB == 1
-#include <curses.h>
-#ifndef NCURSES_VERSION
-#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
-#else
-#define _HAVE_CURSES
-#endif
-#elif _CURSES_LIB == 2
-#include <xcurses.h>
-#define _HAVE_CURSES
-#else
-#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
-#endif
-
-#ifdef _HAVE_CURSES
-#include <ctype.h>
 #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 *)
+#include "bam_tview.h"
 
-char bam_aux_getCEi(bam1_t *b, int i);
-char bam_aux_getCSi(bam1_t *b, int i);
-char bam_aux_getCQi(bam1_t *b, int i);
-
-#define TV_MIN_ALNROW 2
-#define TV_MAX_GOTO  40
-#define TV_LOW_MAPQ  10
+int base_tv_init(tview_t* tv,const char *fn, const char *fn_fa, const char *samples)
+	{
+	assert(tv!=NULL);
+	assert(fn!=NULL);
+	tv->mrow = 24; tv->mcol = 80;
+	tv->color_for = TV_COLOR_MAPQ;
+	tv->is_dot = 1;
+	
+	tv->fp = bam_open(fn, "r");
+	if(tv->fp==0)
+		{
+		fprintf(stderr,"bam_open %s. %s\n", fn,fn_fa);
+            	exit(EXIT_FAILURE);
+		}
+	bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
+	assert(tv->fp);
+	
+	tv->header = bam_header_read(tv->fp);
+	if(tv->header==0)
+		{
+		fprintf(stderr,"Cannot read '%s'.\n", fn);
+            	exit(EXIT_FAILURE);
+		}
+	tv->idx = bam_index_load(fn);
+	if (tv->idx == 0)
+		{
+		fprintf(stderr,"Cannot read index for '%s'.\n", fn);
+		exit(EXIT_FAILURE);
+		}
+	tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
+	if (fn_fa) tv->fai = fai_load(fn_fa);
+	tv->bca = bcf_call_init(0.83, 13);
+	tv->ins = 1;
 
-#define TV_COLOR_MAPQ   0
-#define TV_COLOR_BASEQ  1
-#define TV_COLOR_NUCL   2
-#define TV_COLOR_COL    3
-#define TV_COLOR_COLQ   4
+    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(EXIT_FAILURE);
+        }
+    }
 
-#define TV_BASE_NUCL 0
-#define TV_BASE_COLOR_SPACE 1
+	return 0;
+	}
 
-typedef struct {
-	int mrow, mcol;
-	WINDOW *wgoto, *whelp;
 
-	bam_index_t *idx;
-	bam_lplbuf_t *lplbuf;
-	bam_header_t *header;
-	bamFile fp;
-	int curr_tid, left_pos;
-	faidx_t *fai;
-	bcf_callaux_t *bca;
+void base_tv_destroy(tview_t* tv)
+	{
+	bam_lplbuf_destroy(tv->lplbuf);
+	bcf_call_destroy(tv->bca);
+	bam_index_destroy(tv->idx);
+	if (tv->fai) fai_destroy(tv->fai);
+	free(tv->ref);
+	bam_header_destroy(tv->header);
+	bam_close(tv->fp);
+	}
 
-	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)
 {
@@ -73,11 +87,11 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 	// print referece
 	rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
 	for (i = tv->last_pos + 1; i < pos; ++i) {
-		if (i%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", i+1);
+		if (i%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1);
 		c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
-		mvaddch(1, tv->ccol++, c);
+		tv->my_mvaddch(tv,1, tv->ccol++, c);
 	}
-	if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
+	if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
 	{ // call consensus
 		bcf_callret1_t bcr;
 		int qsum[4], a1, a2, tmp;
@@ -95,15 +109,15 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 		else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
 		else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
 	}
-	attr = A_UNDERLINE;
+	attr = tv->my_underline(tv);
 	c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
 	i = (call&0xffff)/10+1;
 	if (i > 4) i = 4;
-	attr |= COLOR_PAIR(i);
+	attr |= tv->my_colorpair(tv,i);
 	if (c == toupper(rb)) c = '.';
-	attron(attr);
-	mvaddch(2, tv->ccol, c);
-	attroff(attr);
+	tv->my_attron(tv,attr);
+	tv->my_mvaddch(tv,2, tv->ccol, c);
+	tv->my_attroff(tv,attr);
 	if(tv->ins) {
 		// calculate maximum insert
 		for (i = 0; i < n; ++i) {
@@ -153,18 +167,18 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 				int x;
 				attr = 0;
 				if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
-						|| (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
+						|| (p->b->core.flag & BAM_FSECONDARY)) attr |= tv->my_underline(tv);
 				if (tv->color_for == TV_COLOR_BASEQ) {
 					x = bam1_qual(p->b)[p->qpos]/10 + 1;
 					if (x > 4) x = 4;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
 				} else if (tv->color_for == TV_COLOR_MAPQ) {
 					x = p->b->core.qual/10 + 1;
 					if (x > 4) x = 4;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
 				} else if (tv->color_for == TV_COLOR_NUCL) {
 					x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
 				} else if(tv->color_for == TV_COLOR_COL) {
 					x = 0;
 					switch(bam_aux_getCSi(p->b, p->qpos)) {
@@ -176,109 +190,33 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
 						default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
 					}
 					x+=5;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
 				} else if(tv->color_for == TV_COLOR_COLQ) {
 					x = bam_aux_getCQi(p->b, p->qpos);
 					if(0 == x) x = bam1_qual(p->b)[p->qpos];
 					x = x/10 + 1;
 					if (x > 4) x = 4;
-					attr |= COLOR_PAIR(x);
+					attr |= tv->my_colorpair(tv,x);
 				}
-				attron(attr);
-				mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
-				attroff(attr);
+				tv->my_attron(tv,attr);
+				tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
+				tv->my_attroff(tv,attr);
 			}
 		}
 		c = j? '*' : rb;
 		if (c == '*') {
-			attr = COLOR_PAIR(8);
-			attron(attr);
-			mvaddch(1, tv->ccol++, c);
-			attroff(attr);
-		} else mvaddch(1, tv->ccol++, c);
+			attr = tv->my_colorpair(tv,8);
+			tv->my_attron(tv,attr);
+			tv->my_mvaddch(tv,1, tv->ccol++, c);
+			tv->my_attroff(tv,attr);
+		} else tv->my_mvaddch(tv,1, tv->ccol++, c);
 	}
 	tv->last_pos = pos;
 	return 0;
 }
 
-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;
-	tv->fp = bam_open(fn, "r");
-	bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
-	assert(tv->fp);
-	tv->header = bam_header_read(tv->fp);
-	tv->idx = bam_index_load(fn);
-	if (tv->idx == 0) exit(1);
-	tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
-	if (fn_fa) tv->fai = fai_load(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();
-	noecho();
-	cbreak();
-	tv->mrow = 24; tv->mcol = 80;
-	getmaxyx(stdscr, tv->mrow, tv->mcol);
-	tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
-	tv->whelp = newwin(29, 40, 5, 5);
-	tv->color_for = TV_COLOR_MAPQ;
-	start_color();
-	init_pair(1, COLOR_BLUE, COLOR_BLACK);
-	init_pair(2, COLOR_GREEN, COLOR_BLACK);
-	init_pair(3, COLOR_YELLOW, COLOR_BLACK);
-	init_pair(4, COLOR_WHITE, COLOR_BLACK);
-	init_pair(5, COLOR_GREEN, COLOR_BLACK);
-	init_pair(6, COLOR_CYAN, COLOR_BLACK);
-	init_pair(7, COLOR_YELLOW, COLOR_BLACK);
-	init_pair(8, COLOR_RED, COLOR_BLACK);
-	init_pair(9, COLOR_BLUE, COLOR_BLACK);
-	return tv;
-}
-
-void tv_destroy(tview_t *tv)
-{
-	delwin(tv->wgoto); delwin(tv->whelp);
-	endwin();
 
-	bam_lplbuf_destroy(tv->lplbuf);
-	bcf_call_destroy(tv->bca);
-	bam_index_destroy(tv->idx);
-	if (tv->fai) fai_destroy(tv->fai);
-	free(tv->ref);
-	bam_header_destroy(tv->header);
-	bam_close(tv->fp);
-	free(tv);
-}
 
 int tv_fetch_func(const bam1_t *b, void *data)
 {
@@ -302,10 +240,11 @@ int tv_fetch_func(const bam1_t *b, void *data)
 	return 0;
 }
 
-int tv_draw_aln(tview_t *tv, int tid, int pos)
-{
+int base_draw_aln(tview_t *tv, int tid, int pos)
+	{
+	assert(tv!=NULL);
 	// reset
-	clear();
+	tv->my_clear(tv);
 	tv->curr_tid = tid; tv->left_pos = pos;
 	tv->last_pos = tv->left_pos - 1;
 	tv->ccol = 0;
@@ -313,7 +252,10 @@ int tv_draw_aln(tview_t *tv, int tid, int pos)
 	if (tv->fai) {
 		char *str;
 		if (tv->ref) free(tv->ref);
+		assert(tv->curr_tid>=0);
+		
 		str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
+		assert(str!=NULL);
 		sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
 		tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
 		free(str);
@@ -325,144 +267,26 @@ int tv_draw_aln(tview_t *tv, int tid, int pos)
 
 	while (tv->ccol < tv->mcol) {
 		int pos = tv->last_pos + 1;
-		if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
-		mvaddch(1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
+		if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
+		tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
 		++tv->last_pos;
 	}
 	return 0;
 }
 
-static void tv_win_goto(tview_t *tv, int *tid, int *pos)
-{
-	char str[256], *p;
-	int i, l = 0;
-	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
-	mvwprintw(tv->wgoto, 1, 2, "Goto: ");
-	for (;;) {
-		int c = wgetch(tv->wgoto);
-		wrefresh(tv->wgoto);
-		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
-			if(l > 0) --l;
-		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
-			int _tid = -1, _beg, _end;
-			if (str[0] == '=') {
-				_beg = strtol(str+1, &p, 10) - 1;
-				if (_beg > 0) {
-					*pos = _beg;
-					return;
-				}
-			} else {
-				bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
-				if (_tid >= 0) {
-					*tid = _tid; *pos = _beg;
-					return;
-				}
-			}
-		} else if (isgraph(c)) {
-			if (l < TV_MAX_GOTO) str[l++] = c;
-		} else if (c == '\027') l = 0;
-		else if (c == '\033') return;
-		str[l] = '\0';
-		for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
-		mvwprintw(tv->wgoto, 1, 8, "%s", str);
-	}
-}
 
-static void tv_win_help(tview_t *tv) {
-	int r = 1;
-	WINDOW *win = tv->whelp;
-	wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
-	mvwprintw(win, r++, 2, "        -=-    Help    -=- ");
-	r++;
-	mvwprintw(win, r++, 2, "?          This window");
-	mvwprintw(win, r++, 2, "Arrows     Small scroll movement");
-	mvwprintw(win, r++, 2, "h,j,k,l    Small scroll movement");
-	mvwprintw(win, r++, 2, "H,J,K,L    Large scroll movement");
-	mvwprintw(win, r++, 2, "ctrl-H     Scroll 1k left");
-	mvwprintw(win, r++, 2, "ctrl-L     Scroll 1k right");
-	mvwprintw(win, r++, 2, "space      Scroll one screen");
-	mvwprintw(win, r++, 2, "backspace  Scroll back one screen");
-	mvwprintw(win, r++, 2, "g          Go to specific location");
-	mvwprintw(win, r++, 2, "m          Color for mapping qual");
-	mvwprintw(win, r++, 2, "n          Color for nucleotide");
-	mvwprintw(win, r++, 2, "b          Color for base quality");
-	mvwprintw(win, r++, 2, "c          Color for cs color");
-	mvwprintw(win, r++, 2, "z          Color for cs qual");
-	mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
-	mvwprintw(win, r++, 2, "s          Toggle on/off ref skip");
-	mvwprintw(win, r++, 2, "r          Toggle on/off rd name");
-	mvwprintw(win, r++, 2, "N          Turn on nt view");
-	mvwprintw(win, r++, 2, "C          Turn on cs view");
-	mvwprintw(win, r++, 2, "i          Toggle on/off ins");
-	mvwprintw(win, r++, 2, "q          Exit");
-	r++;
-	mvwprintw(win, r++, 2, "Underline:      Secondary or orphan");
-	mvwprintw(win, r++, 2, "Blue:    0-9    Green: 10-19");
-	mvwprintw(win, r++, 2, "Yellow: 20-29   White: >=30");
-	wrefresh(win);
-	wgetch(win);
-}
 
-void tv_loop(tview_t *tv)
-{
-	int tid, pos;
-	tid = tv->curr_tid; pos = tv->left_pos;
-	while (1) {
-		int c = getch();
-		switch (c) {
-			case '?': tv_win_help(tv); break;
-			case '\033':
-			case 'q': goto end_loop;
-			case '/': 
-			case 'g': tv_win_goto(tv, &tid, &pos); break;
-			case 'm': tv->color_for = TV_COLOR_MAPQ; break;
-			case 'b': tv->color_for = TV_COLOR_BASEQ; break;
-			case 'n': tv->color_for = TV_COLOR_NUCL; break;
-			case 'c': tv->color_for = TV_COLOR_COL; break;
-			case 'z': tv->color_for = TV_COLOR_COLQ; break;
-			case 's': tv->no_skip = !tv->no_skip; break;
-			case 'r': tv->show_name = !tv->show_name; break;
-			case KEY_LEFT:
-			case 'h': --pos; break;
-			case KEY_RIGHT:
-			case 'l': ++pos; break;
-			case KEY_SLEFT:
-			case 'H': pos -= 20; break;
-			case KEY_SRIGHT:
-			case 'L': pos += 20; break;
-			case '.': tv->is_dot = !tv->is_dot; break;
-			case 'N': tv->base_for = TV_BASE_NUCL; break;
-			case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
-			case 'i': tv->ins = !tv->ins; break;
-			case '\010': pos -= 1000; break;
-			case '\014': pos += 1000; break;
-			case ' ': pos += tv->mcol; break;
-			case KEY_UP:
-			case 'j': --tv->row_shift; break;
-			case KEY_DOWN:
-			case 'k': ++tv->row_shift; break;
-			case KEY_BACKSPACE:
-			case '\177': pos -= tv->mcol; break;
-			case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
-			default: continue;
-		}
-		if (pos < 0) pos = 0;
-		if (tv->row_shift < 0) tv->row_shift = 0;
-		tv_draw_aln(tv, tid, pos);
-	}
-end_loop:
-	return;
-}
 
-void error(const char *format, ...)
+static 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, "   -d display      output as (H)tml or (C)urses or (T)ext \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, "   -s STR          display only reads from this sample or group\n");
         fprintf(stderr, "\n\n");
     }
     else
@@ -475,38 +299,70 @@ void error(const char *format, ...)
     exit(-1);
 }
 
+enum dipsay_mode {display_ncurses,display_html,display_text};
+extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
 
 int bam_tview_main(int argc, char *argv[])
-{
-	tview_t *tv;
+	{
+	int view_mode=display_ncurses;
+	tview_t* tv=NULL;
     char *samples=NULL, *position=NULL;
     int c;
-    while ((c = getopt(argc, argv, "s:p:")) >= 0) {
+    while ((c = getopt(argc, argv, "s:p:d:")) >= 0) {
         switch (c) {
             case 's': samples=optarg; break;
             case 'p': position=optarg; break;
+            case 'd':
+            	{
+            	switch(optarg[0])
+            		{
+            		case 'H': case 'h': view_mode=display_html;break;
+            		case 'T': case 't': view_mode=display_text;break;
+            		case 'C': case 'c': view_mode=display_ncurses;break;
+			default: view_mode=display_ncurses;break;
+			}
+            	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;
-}
-#else // #ifdef _HAVE_CURSES
-#include <stdio.h>
-#warning "No curses library is available; tview is disabled."
-int bam_tview_main(int argc, char *argv[])
-{
-	fprintf(stderr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");
-	return 1;
-}
-#endif // #ifdef _HAVE_CURSES
+	
+	switch(view_mode)
+		{
+		case display_ncurses:
+			{
+			tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+			break;
+			}
+		case display_text:
+			{
+			tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+			break;
+			}
+		case display_html:
+			{
+			tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+			break;
+			}
+		}
+	if(tv==NULL)
+		{
+		error("cannot create view");
+		return EXIT_FAILURE;
+		}
+	
+	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->my_drawaln(tv, tv->curr_tid, tv->left_pos);
+	tv->my_loop(tv);
+	tv->my_destroy(tv);
+	
+	return EXIT_SUCCESS;
+	}
diff --git a/bam_tview.h b/bam_tview.h
new file mode 100644
index 0000000..80f0464
--- /dev/null
+++ b/bam_tview.h
@@ -0,0 +1,75 @@
+#ifndef BAM_TVIEW_H
+#define BAM_TVIEW_H
+
+#include <ctype.h>
+#include <assert.h>
+#include <string.h>
+#include <math.h>
+#include <unistd.h>
+#include <stdarg.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 *)
+
+typedef struct AbstractTview {
+	int mrow, mcol;
+	
+	bam_index_t *idx;
+	bam_lplbuf_t *lplbuf;
+	bam_header_t *header;
+	bamFile fp;
+	int curr_tid, left_pos;
+	faidx_t *fai;
+	bcf_callaux_t *bca;
+
+	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;
+    /* callbacks */
+    void (*my_destroy)(struct AbstractTview* );
+    void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+    void (*my_mvaddch)(struct AbstractTview*,int,int,int);
+    void (*my_attron)(struct AbstractTview*,int);
+    void (*my_attroff)(struct AbstractTview*,int);
+    void (*my_clear)(struct AbstractTview*);
+    int (*my_colorpair)(struct AbstractTview*,int);
+    int (*my_drawaln)(struct AbstractTview*,int,int);
+    int (*my_loop)(struct AbstractTview*);
+    int (*my_underline)(struct AbstractTview*);
+} tview_t;
+
+
+char bam_aux_getCEi(bam1_t *b, int i);
+char bam_aux_getCSi(bam1_t *b, int i);
+char bam_aux_getCQi(bam1_t *b, int i);
+
+#define TV_MIN_ALNROW 2
+#define TV_MAX_GOTO  40
+#define TV_LOW_MAPQ  10
+
+#define TV_COLOR_MAPQ   0
+#define TV_COLOR_BASEQ  1
+#define TV_COLOR_NUCL   2
+#define TV_COLOR_COL    3
+#define TV_COLOR_COLQ   4
+
+#define TV_BASE_NUCL 0
+#define TV_BASE_COLOR_SPACE 1
+
+int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
+int base_tv_init(tview_t*,const char *fn, const char *fn_fa, const char *samples);
+void base_tv_destroy(tview_t*);
+int base_draw_aln(tview_t *tv, int tid, int pos);
+
+typedef struct Tixel
+	{
+	int ch;
+	int attributes;
+	}tixel_t;
+
+#endif
+
diff --git a/bam_tview_curses.c b/bam_tview_curses.c
new file mode 100644
index 0000000..4fdd1fb
--- /dev/null
+++ b/bam_tview_curses.c
@@ -0,0 +1,297 @@
+#undef _HAVE_CURSES
+
+#if _CURSES_LIB == 0
+#elif _CURSES_LIB == 1
+#include <curses.h>
+#ifndef NCURSES_VERSION
+#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
+#else
+#define _HAVE_CURSES
+#endif
+#elif _CURSES_LIB == 2
+#include <xcurses.h>
+#define _HAVE_CURSES
+#else
+#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
+#endif
+
+
+#include "bam_tview.h"
+
+#ifdef _HAVE_CURSES
+
+
+
+typedef struct CursesTview {
+	tview_t view;
+	WINDOW *wgoto, *whelp;
+	} curses_tview_t;
+
+
+
+
+#define FROM_TV(ptr) ((curses_tview_t*)ptr)
+
+static void curses_destroy(tview_t* base)
+	{
+	curses_tview_t* tv=(curses_tview_t*)base;
+
+	
+	delwin(tv->wgoto); delwin(tv->whelp);
+	endwin();
+
+	base_tv_destroy(base);
+	
+	free(tv);
+	}
+
+/*
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+    void (*my_)(struct AbstractTview*,int,int,int);
+    void (*my_attron)(struct AbstractTview*,int);
+    void (*my_attroff)(struct AbstractTview*,int);
+    void (*my_clear)(struct AbstractTview*);
+    int (*my_colorpair)(struct AbstractTview*,int);
+*/
+
+static void curses_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
+	{
+	unsigned int size=tv->mcol+2;
+	char* str=malloc(size);
+	if(str==0) exit(EXIT_FAILURE);
+	va_list argptr;
+  	va_start(argptr, fmt);
+	vsnprintf(str,size, fmt, argptr);
+	va_end(argptr);
+	mvprintw(y,x,str);
+	free(str);
+	}
+
+static void curses_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
+	{
+	mvaddch(y,x,ch);
+	}
+    	
+static void curses_attron(struct AbstractTview* tv,int flag)
+    {
+    attron(flag);
+    }
+static void curses_attroff(struct AbstractTview* tv,int flag)
+    {
+    attroff(flag);
+    }
+static void curses_clear(struct AbstractTview* tv)
+    {
+    clear();
+    }
+    
+static int curses_colorpair(struct AbstractTview* tv,int flag)
+    {
+    return COLOR_PAIR(flag);
+    }
+
+static int curses_drawaln(struct AbstractTview* tv, int tid, int pos)
+    {
+    return base_draw_aln(tv,  tid, pos);
+    }
+
+
+
+static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
+	{
+	char str[256], *p;
+	int i, l = 0;
+	tview_t *base=(tview_t*)tv;
+	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
+	mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+	for (;;) {
+		int c = wgetch(tv->wgoto);
+		wrefresh(tv->wgoto);
+		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
+			if(l > 0) --l;
+		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
+			int _tid = -1, _beg, _end;
+			if (str[0] == '=') {
+				_beg = strtol(str+1, &p, 10) - 1;
+				if (_beg > 0) {
+					*pos = _beg;
+					return;
+				}
+			} else {
+				bam_parse_region(base->header, str, &_tid, &_beg, &_end);
+				if (_tid >= 0) {
+					*tid = _tid; *pos = _beg;
+					return;
+				}
+			}
+		} else if (isgraph(c)) {
+			if (l < TV_MAX_GOTO) str[l++] = c;
+		} else if (c == '\027') l = 0;
+		else if (c == '\033') return;
+		str[l] = '\0';
+		for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
+		mvwprintw(tv->wgoto, 1, 8, "%s", str);
+	}
+}
+
+
+
+
+static void tv_win_help(curses_tview_t *tv) {
+	int r = 1;
+	tview_t* base=(tview_t*)base;
+	WINDOW *win = tv->whelp;
+	wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
+	mvwprintw(win, r++, 2, "        -=-    Help    -=- ");
+	r++;
+	mvwprintw(win, r++, 2, "?          This window");
+	mvwprintw(win, r++, 2, "Arrows     Small scroll movement");
+	mvwprintw(win, r++, 2, "h,j,k,l    Small scroll movement");
+	mvwprintw(win, r++, 2, "H,J,K,L    Large scroll movement");
+	mvwprintw(win, r++, 2, "ctrl-H     Scroll 1k left");
+	mvwprintw(win, r++, 2, "ctrl-L     Scroll 1k right");
+	mvwprintw(win, r++, 2, "space      Scroll one screen");
+	mvwprintw(win, r++, 2, "backspace  Scroll back one screen");
+	mvwprintw(win, r++, 2, "g          Go to specific location");
+	mvwprintw(win, r++, 2, "m          Color for mapping qual");
+	mvwprintw(win, r++, 2, "n          Color for nucleotide");
+	mvwprintw(win, r++, 2, "b          Color for base quality");
+	mvwprintw(win, r++, 2, "c          Color for cs color");
+	mvwprintw(win, r++, 2, "z          Color for cs qual");
+	mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
+	mvwprintw(win, r++, 2, "s          Toggle on/off ref skip");
+	mvwprintw(win, r++, 2, "r          Toggle on/off rd name");
+	mvwprintw(win, r++, 2, "N          Turn on nt view");
+	mvwprintw(win, r++, 2, "C          Turn on cs view");
+	mvwprintw(win, r++, 2, "i          Toggle on/off ins");
+	mvwprintw(win, r++, 2, "q          Exit");
+	r++;
+	mvwprintw(win, r++, 2, "Underline:      Secondary or orphan");
+	mvwprintw(win, r++, 2, "Blue:    0-9    Green: 10-19");
+	mvwprintw(win, r++, 2, "Yellow: 20-29   White: >=30");
+	wrefresh(win);
+	wgetch(win);
+}
+
+static int curses_underline(tview_t* tv)
+	{
+	return A_UNDERLINE;
+	}
+	
+static int curses_loop(tview_t* tv)
+	{
+	int tid, pos;
+	curses_tview_t *CTV=(curses_tview_t *)tv;
+	tid = tv->curr_tid; pos = tv->left_pos;
+	while (1) {
+		int c = getch();
+		switch (c) {
+			case '?': tv_win_help(CTV); break;
+			case '\033':
+			case 'q': goto end_loop;
+			case '/': 
+			case 'g': tv_win_goto(CTV, &tid, &pos); break;
+			case 'm': tv->color_for = TV_COLOR_MAPQ; break;
+			case 'b': tv->color_for = TV_COLOR_BASEQ; break;
+			case 'n': tv->color_for = TV_COLOR_NUCL; break;
+			case 'c': tv->color_for = TV_COLOR_COL; break;
+			case 'z': tv->color_for = TV_COLOR_COLQ; break;
+			case 's': tv->no_skip = !tv->no_skip; break;
+			case 'r': tv->show_name = !tv->show_name; break;
+			case KEY_LEFT:
+			case 'h': --pos; break;
+			case KEY_RIGHT:
+			case 'l': ++pos; break;
+			case KEY_SLEFT:
+			case 'H': pos -= 20; break;
+			case KEY_SRIGHT:
+			case 'L': pos += 20; break;
+			case '.': tv->is_dot = !tv->is_dot; break;
+			case 'N': tv->base_for = TV_BASE_NUCL; break;
+			case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
+			case 'i': tv->ins = !tv->ins; break;
+			case '\010': pos -= 1000; break;
+			case '\014': pos += 1000; break;
+			case ' ': pos += tv->mcol; break;
+			case KEY_UP:
+			case 'j': --tv->row_shift; break;
+			case KEY_DOWN:
+			case 'k': ++tv->row_shift; break;
+			case KEY_BACKSPACE:
+			case '\177': pos -= tv->mcol; break;
+			case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+			default: continue;
+		}
+		if (pos < 0) pos = 0;
+		if (tv->row_shift < 0) tv->row_shift = 0;
+		tv->my_drawaln(tv, tid, pos);
+	}
+end_loop:
+	return 0;
+}
+
+
+
+
+tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+	{
+	curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
+	tview_t* base=(tview_t*)tv;
+	if(tv==0)
+		{
+		fprintf(stderr,"Calloc failed\n");
+		return 0;
+		}
+	
+	base_tv_init(base,fn,fn_fa,samples);
+	/* initialize callbacks */
+#define SET_CALLBACK(fun) base->my_##fun=curses_##fun;
+	SET_CALLBACK(destroy);
+	SET_CALLBACK(mvprintw);
+	SET_CALLBACK(mvaddch);
+	SET_CALLBACK(attron);
+	SET_CALLBACK(attroff);
+	SET_CALLBACK(clear);
+	SET_CALLBACK(colorpair);
+	SET_CALLBACK(drawaln);
+	SET_CALLBACK(loop);
+	SET_CALLBACK(underline);
+#undef SET_CALLBACK
+
+	initscr();
+	keypad(stdscr, TRUE);
+	clear();
+	noecho();
+	cbreak();
+	
+	getmaxyx(stdscr, base->mrow, base->mcol);
+	tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
+	tv->whelp = newwin(29, 40, 5, 5);
+	
+	start_color();
+	init_pair(1, COLOR_BLUE, COLOR_BLACK);
+	init_pair(2, COLOR_GREEN, COLOR_BLACK);
+	init_pair(3, COLOR_YELLOW, COLOR_BLACK);
+	init_pair(4, COLOR_WHITE, COLOR_BLACK);
+	init_pair(5, COLOR_GREEN, COLOR_BLACK);
+	init_pair(6, COLOR_CYAN, COLOR_BLACK);
+	init_pair(7, COLOR_YELLOW, COLOR_BLACK);
+	init_pair(8, COLOR_RED, COLOR_BLACK);
+	init_pair(9, COLOR_BLUE, COLOR_BLACK);
+	return base;
+	}
+
+
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; tview with curses is disabled."
+
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
+
+tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+	{
+	return text_tv_init(fn,fn_fa,samples);
+	}
+#endif // #ifdef _HAVE_CURSES
+
+	
diff --git a/bam_tview_html.c b/bam_tview_html.c
new file mode 100644
index 0000000..f52b4c3
--- /dev/null
+++ b/bam_tview_html.c
@@ -0,0 +1,349 @@
+#include <unistd.h>
+#include "bam_tview.h"
+
+#define UNDERLINE_FLAG 10
+
+typedef struct HtmlTview {
+	tview_t view;
+	int row_count;
+	tixel_t** screen;
+	FILE* out;
+	int attributes;/* color... */
+	} html_tview_t;
+
+#define FROM_TV(ptr) ((html_tview_t*)ptr)
+
+static void html_destroy(tview_t* base)
+	{
+	int i;
+	html_tview_t* tv=(html_tview_t*)base;
+	if(tv->screen!=NULL)
+		{
+		for(i=0;i< tv->row_count;++i) free(tv->screen[i]);
+		free(tv->screen);
+		}
+	base_tv_destroy(base);
+	free(tv);
+	}
+
+/*
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+    void (*my_)(struct AbstractTview*,int,int,int);
+    void (*my_attron)(struct AbstractTview*,int);
+    void (*my_attroff)(struct AbstractTview*,int);
+    void (*my_clear)(struct AbstractTview*);
+    int (*my_colorpair)(struct AbstractTview*,int);
+*/
+
+static void html_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
+	{
+	int i,nchars=0;
+	unsigned int size=tv->mcol+2;
+	char* str=malloc(size);
+	if(str==0) exit(EXIT_FAILURE);
+	va_list argptr;
+  	va_start(argptr, fmt);
+	nchars=vsnprintf(str,size, fmt, argptr);
+	va_end(argptr);
+	
+	for(i=0;i< nchars;++i)
+		{
+		tv->my_mvaddch(tv,y,x+i,str[i]);
+		}
+	free(str);
+	}
+
+static void html_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
+	{
+	tixel_t* row=NULL;
+	html_tview_t* ptr=FROM_TV(tv);
+	if( x >= tv->mcol ) return; //out of screen
+	while(ptr->row_count<=y)
+		{
+		int x;
+		row=(tixel_t*)calloc(tv->mcol,sizeof(tixel_t));
+		if(row==0)  exit(EXIT_FAILURE);
+		for(x=0;x<tv->mcol;++x) {row[x].ch=' ';row[x].attributes=0;}
+		ptr->screen=(tixel_t**)realloc(ptr->screen,sizeof(tixel_t*)*(ptr->row_count+1));
+		ptr->screen[ptr->row_count++]=row;
+		}
+	row=ptr->screen[y];
+	row[x].ch=ch;
+	row[x].attributes=ptr->attributes;
+	}
+    	
+static void html_attron(struct AbstractTview* tv,int flag)
+    {
+    html_tview_t* ptr=FROM_TV(tv);
+    ptr->attributes |=  flag;
+
+
+    }
+   
+static void html_attroff(struct AbstractTview* tv,int flag)
+    {
+    html_tview_t* ptr=FROM_TV(tv);
+    ptr->attributes &= ~(flag);
+    }
+    
+static void html_clear(struct AbstractTview* tv)
+    {
+    html_tview_t* ptr=FROM_TV(tv);
+    if(ptr->screen!=NULL)
+	{
+	int i;
+	for(i=0;i< ptr->row_count;++i) free(ptr->screen[i]);
+	free(ptr->screen);
+	ptr->screen=NULL;
+	}
+    ptr->row_count=0;
+    ptr->attributes=0;
+    }
+    
+static int html_colorpair(struct AbstractTview* tv,int flag)
+    {
+    return (1 << (flag));
+    }
+
+static int html_drawaln(struct AbstractTview* tv, int tid, int pos)
+    {
+    int y,x;
+    html_tview_t* ptr=FROM_TV(tv);
+    html_clear(tv);
+    base_draw_aln(tv,  tid, pos);
+    fputs("<html><head>",ptr->out);
+    fprintf(ptr->out,"<title>%s:%d</title>",
+    	tv->header->target_name[tid],
+    	pos+1
+    	);
+    //style
+   
+    fputs("<style type='text/css'>\n",ptr->out);
+    fputs(".tviewbody { margin:5px; background-color:white;text-align:center;}\n",ptr->out);
+    fputs(".tviewtitle {text-align:center;}\n",ptr->out);
+    fputs(".tviewpre { margin:5px; background-color:white;}\n",ptr->out);
+    #define CSS(id,col) fprintf(ptr->out,".tviewc%d {color:%s;}\n.tviewcu%d {color:%s;text-decoration:underline;}\n",id,col,id,col);
+        CSS(0, "black");
+    	CSS(1, "blue");
+	CSS(2, "green");
+	CSS(3, "yellow");
+	CSS(4, "black");
+	CSS(5, "green");
+	CSS(6, "cyan");
+	CSS(7, "yellow");
+	CSS(8, "red");
+	CSS(9, "blue");
+    #undef CSS
+    fputs("</style>",ptr->out);
+    
+    fputs("</head><body>",ptr->out);
+    
+      fprintf(ptr->out,"<div class='tviewbody'><div class='tviewtitle'>%s:%d</div>",
+    	tv->header->target_name[tid],
+    	pos+1
+    	);
+    
+    fputs("<pre class='tviewpre'>",ptr->out);
+    for(y=0;y< ptr->row_count;++y)
+    	{
+    	
+    	for(x=0;x< tv->mcol;++x)
+	    	{
+	    	
+		
+		if(x== 0 || ptr->screen[y][x].attributes != ptr->screen[y][x-1].attributes)
+	    		{
+	    		int css=0;
+			fprintf(ptr->out,"<span");
+	    		while(css<32)
+	    			{
+	    			//if(y>1) fprintf(stderr,"css=%d pow2=%d vs %d\n",css,(1 << (css)),ptr->screen[y][x].attributes);
+	    			if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0)
+	    				{
+	    				
+	    				fprintf(ptr->out," class='tviewc%s%d'",
+	    					(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)) )!=0?"u":""),
+	    					css);
+	    				break;
+	    				}
+	    			++css;
+	    			}
+
+
+	    		fputs(">",ptr->out);
+	    		}
+		
+		int ch=ptr->screen[y][x].ch;
+		switch(ch)
+			{
+			case '<': fputs("&lt;",ptr->out);break;
+			case '>': fputs("&gt;",ptr->out);break;
+			case '&': fputs("&amp;",ptr->out);break;
+			default: fputc(ch,ptr->out); break;
+			}
+	    	
+	    	
+	    	if(x+1 == tv->mcol  || ptr->screen[y][x].attributes!=ptr->screen[y][x+1].attributes)
+	    		{
+	    		fputs("</span>",ptr->out);
+	    		}
+	    	}
+    	if(y+1 < ptr->row_count) fputs("<br/>",ptr->out);
+    	}
+    fputs("</pre></div></body></html>",ptr->out);
+    return 0;
+    }
+
+
+#define ANSI_COLOR_RED "\x1b[31m"
+#define ANSI_COLOR_GREEN "\x1b[32m"
+#define ANSI_COLOR_YELLOW "\x1b[33m"
+#define ANSI_COLOR_BLUE "\x1b[34m"
+#define ANSI_COLOR_MAGENTA "\x1b[35m"
+#define ANSI_COLOR_CYAN "\x1b[36m"
+#define ANSI_COLOR_BLACK "\x1b[0m"
+#define ANSI_COLOR_RESET ANSI_COLOR_BLACK
+
+#define ANSI_UNDERLINE_SET "\033[4m"
+#define ANSI_UNDERLINE_UNSET "\033[0m"
+
+static int text_drawaln(struct AbstractTview* tv, int tid, int pos)
+    {
+    int y,x;
+    html_tview_t* ptr=FROM_TV(tv);
+    html_clear(tv);
+    base_draw_aln(tv,  tid, pos); 
+    int is_term= isatty(fileno(ptr->out));
+    
+    for(y=0;y< ptr->row_count;++y)
+    	{
+    	for(x=0;x< tv->mcol;++x)
+	    	{
+	    	if(is_term)
+	    		{
+	    		int css=0;
+	    		while(css<32)
+	    			{
+	    			if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0)
+	    				{
+	    				break;
+	    				}
+	    			++css;
+	    			}
+    			switch(css)
+    				{
+    				//CSS(0, "black");
+			    	case 1: fputs(ANSI_COLOR_BLUE,ptr->out); break;
+				case 2: fputs(ANSI_COLOR_GREEN,ptr->out); break;
+				case 3: fputs(ANSI_COLOR_YELLOW,ptr->out); break;
+				//CSS(4, "black");
+				case 5: fputs(ANSI_COLOR_GREEN,ptr->out); break;
+				case 6: fputs(ANSI_COLOR_CYAN,ptr->out); break;
+				case 7: fputs(ANSI_COLOR_YELLOW,ptr->out); break;
+				case 8: fputs(ANSI_COLOR_RED,ptr->out); break;
+				case 9: fputs(ANSI_COLOR_BLUE,ptr->out); break;
+				default:break;
+    				}
+    			if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0)
+    				{
+    				fputs(ANSI_UNDERLINE_SET,ptr->out);
+    				}
+    			
+	    		}
+	    	
+	    	
+	    	int ch=ptr->screen[y][x].ch;
+
+	    	fputc(ch,ptr->out);
+	    	if(is_term)
+	    		{
+	    		fputs(ANSI_COLOR_RESET,ptr->out);
+	    		if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0)
+    				{
+    				fputs(ANSI_UNDERLINE_UNSET,ptr->out);
+    				}
+	    		}
+	    	}
+    	fputc('\n',ptr->out);
+    	}
+    return 0;
+    }
+
+
+static int html_loop(tview_t* tv)
+	{
+	//tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
+	return 0;	
+	}
+
+static int html_underline(tview_t* tv)
+	{
+	return (1 << UNDERLINE_FLAG);	
+	}
+
+/*
+static void init_pair(html_tview_t *tv,int id_ge_1, const char* pen, const char* paper)
+	{
+	
+	}
+*/
+
+tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples)
+	{
+	char* colstr=getenv("COLUMNS");
+	html_tview_t *tv = (html_tview_t*)calloc(1, sizeof(html_tview_t));
+	tview_t* base=(tview_t*)tv;
+	if(tv==0)
+		{
+		fprintf(stderr,"Calloc failed\n");
+		return 0;
+		}
+	tv->row_count=0;
+	tv->screen=NULL;
+	tv->out=stdout;
+	tv->attributes=0;
+	base_tv_init(base,fn,fn_fa,samples);
+	/* initialize callbacks */
+#define SET_CALLBACK(fun) base->my_##fun=html_##fun;
+	SET_CALLBACK(destroy);
+	SET_CALLBACK(mvprintw);
+	SET_CALLBACK(mvaddch);
+	SET_CALLBACK(attron);
+	SET_CALLBACK(attroff);
+	SET_CALLBACK(clear);
+	SET_CALLBACK(colorpair);
+	SET_CALLBACK(drawaln);
+	SET_CALLBACK(loop);
+	SET_CALLBACK(underline);
+#undef SET_CALLBACK
+
+	
+	if(colstr!=0)
+		{
+		base->mcol=atoi(colstr);
+		if(base->mcol<10) base->mcol=80;
+		}
+	base->mrow=99999;
+	
+/*
+	init_pair(tv,1, "blue", "white");
+	init_pair(tv,2, "green", "white");
+	init_pair(tv,3, "yellow", "white");
+	init_pair(tv,4, "white", "white");
+	init_pair(tv,5, "green", "white");
+	init_pair(tv,6, "cyan", "white");
+	init_pair(tv,7, "yellow", "white");
+	init_pair(tv,8, "red", "white");
+	init_pair(tv,9, "blue", "white");
+	*/
+	return base;
+	}
+
+
+tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples)
+	{
+	tview_t* tv=html_tv_init(fn,fn_fa,samples);
+	tv->my_drawaln=text_drawaln;
+	return tv;
+	}
+
diff --git a/bcftools/call1.c b/bcftools/call1.c
index eb58498..18805a0 100644
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -328,6 +328,9 @@ int bcfview(int argc, char *argv[])
 	extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
 	extern int bcf_pair_call(const bcf1_t *b);
 	extern int bcf_min_diff(const bcf1_t *b);
+	extern int bcf_p1_get_M(bcf_p1aux_t *b);
+
+	extern gzFile bcf_p1_fp_lk;
 
 	bcf_t *bp, *bout = 0;
 	bcf1_t *b, *blast;
@@ -343,10 +346,10 @@ int bcfview(int argc, char *argv[])
 	memset(&vc, 0, sizeof(viewconf_t));
 	vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1; vc.min_ma_lrt = -1;
 	memset(qcnt, 0, 8 * 256);
-	while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:")) >= 0) {
+	while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
 		switch (c) {
 		case '1': vc.n1 = atoi(optarg); break;
-		case 'l': vc.bed = bed_read(optarg); break;
+		case 'l': vc.bed = bed_read(optarg); if (!vc.bed) fprintf(stderr,"Could not read \"%s\"\n", optarg); return 1; break;
 		case 'D': vc.fn_dict = strdup(optarg); break;
 		case 'F': vc.flag |= VC_FIX_PL; break;
 		case 'N': vc.flag |= VC_ACGT_ONLY; break;
@@ -373,6 +376,7 @@ int bcfview(int argc, char *argv[])
 		case 'C': vc.min_lrt = atof(optarg); break;
 		case 'X': vc.min_perm_p = atof(optarg); break;
 		case 'd': vc.min_smpl_frac = atof(optarg); break;
+		case 'K': bcf_p1_fp_lk = gzopen(optarg, "w"); break;
 		case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
 			vc.ploidy = calloc(vc.n_sub + 1, 1);
 			for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
@@ -462,7 +466,7 @@ int bcfview(int argc, char *argv[])
 			vc.sublist = calloc(vc.n_sub, sizeof(int));
 			hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
 		}
-		if (vc.flag & VC_CALL) write_header(hout);
+		write_header(hout); // always print the header
 		vcf_hdr_write(bout, hout);
 	}
 	if (vc.flag & VC_CALL) {
@@ -496,6 +500,10 @@ int bcfview(int argc, char *argv[])
 			}
 		}
 	}
+	if (bcf_p1_fp_lk && p1) {
+		int32_t M = bcf_p1_get_M(p1);
+		gzwrite(bcf_p1_fp_lk, &M, 4);
+	}
 	while (vcf_read(bp, hin, b) > 0) {
 		int is_indel, cons_llr = -1;
 		int64_t cons_gt = -1;
@@ -544,7 +552,7 @@ int bcfview(int argc, char *argv[])
 			int i;
 			for (i = 0; i < 9; ++i) em[i] = -1.;
 		}
-        if ( !(vc.flag&VC_KEEPALT) && vc.flag&VC_CALL && vc.min_ma_lrt>=0 )
+        if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
         {
             bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
             int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY);
@@ -552,7 +560,11 @@ int bcfview(int argc, char *argv[])
         }
 		else if (vc.flag & VC_CALL) { // call variants
 			bcf_p1rst_t pr;
-			int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
+			int calret;
+			gzwrite(bcf_p1_fp_lk, &b->tid, 4);
+			gzwrite(bcf_p1_fp_lk, &b->pos, 4);
+			gzwrite(bcf_p1_fp_lk, &em[0], sizeof(double));
+			calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
 			if (n_processed % 100000 == 0) {
 				fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
 				bcf_p1_dump_afs(p1);
@@ -597,6 +609,8 @@ int bcfview(int argc, char *argv[])
 		} else bcf_fix_gt(b);
 		vcf_write(bout, hout, b);
 	}
+
+	if (bcf_p1_fp_lk) gzclose(bcf_p1_fp_lk);
 	if (vc.prior_file) free(vc.prior_file);
 	if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
 	if (hin != hout) bcf_hdr_destroy(hout);
diff --git a/bcftools/index.c b/bcftools/index.c
index 014856d..a7db24f 100644
--- a/bcftools/index.c
+++ b/bcftools/index.c
@@ -259,6 +259,7 @@ int bcf_idx_build2(const char *fn, const char *_fnidx)
 	if (fpidx == 0) {
 		fprintf(stderr, "[bcf_idx_build2] fail to create the index file.\n");
 		free(fnidx);
+        bcf_idx_destroy(idx);
 		return -1;
 	}
 	bcf_idx_save(idx, fpidx);
diff --git a/bcftools/prob1.c b/bcftools/prob1.c
index d655722..f04cf08 100644
--- a/bcftools/prob1.c
+++ b/bcftools/prob1.c
@@ -5,6 +5,7 @@
 #include <errno.h>
 #include <assert.h>
 #include <limits.h>
+#include <zlib.h>
 #include "prob1.h"
 #include "kstring.h"
 
@@ -15,6 +16,8 @@ KSTREAM_INIT(gzFile, gzread, 16384)
 #define MC_EM_EPS 1e-5
 #define MC_DEF_INDEL 0.15
 
+gzFile bcf_p1_fp_lk;
+
 unsigned char seq_nt4_table[256] = {
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
@@ -165,6 +168,8 @@ bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy)
 	return ma;
 }
 
+int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; }
+
 int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
 {
 	if (n1 == 0 || n1 >= b->n) return -1;
@@ -751,6 +756,8 @@ static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
 		}
 	}
 	if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
+	if (bcf_p1_fp_lk)
+		gzwrite(bcf_p1_fp_lk, ma->z, sizeof(double) * (ma->M + 1));
 }
 
 static void mc_cal_y(bcf_p1aux_t *ma)
diff --git a/bcftools/vcf.c b/bcftools/vcf.c
index bc11084..e8526a3 100644
--- a/bcftools/vcf.c
+++ b/bcftools/vcf.c
@@ -30,7 +30,12 @@ bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
 	memset(&smpl, 0, sizeof(kstring_t));
 	while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
 		if (v->line.l < 2) continue;
-		if (v->line.s[0] != '#') return 0; // no sample line
+		if (v->line.s[0] != '#') {
+            free(meta.s);
+            free(smpl.s);
+            free(h);
+            return 0; // no sample line
+        }
 		if (v->line.s[0] == '#' && v->line.s[1] == '#') {
 			kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
 		} else if (v->line.s[0] == '#') {
diff --git a/ksort.h b/ksort.h
index fa850ab..aa0bb93 100644
--- a/ksort.h
+++ b/ksort.h
@@ -26,6 +26,10 @@
 /* Contact: Heng Li <lh3@sanger.ac.uk> */
 
 /*
+  2012-12-11 (0.1.4):
+
+    * Defined __ks_insertsort_##name as static to compile with C99.
+
   2008-11-16 (0.1.4):
 
     * Fixed a bug in introsort() that happens in rare cases.
@@ -141,7 +145,7 @@ typedef struct {
 			tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
 		}																\
 	}																	\
-	inline void __ks_insertsort_##name(type_t *s, type_t *t)			\
+	static inline void __ks_insertsort_##name(type_t *s, type_t *t)		\
 	{																	\
 		type_t *i, *j, swap_tmp;										\
 		for (i = s + 1; i < t; ++i)										\
diff --git a/misc/Makefile b/misc/Makefile
index e1a5add..d36e7ac 100644
--- a/misc/Makefile
+++ b/misc/Makefile
@@ -28,7 +28,7 @@ lib-recur all-recur clean-recur cleanlocal-recur install-recur:
 lib:
 
 bamcheck:bamcheck.o
-		$(CC) $(CFLAGS) -o $@ bamcheck.o -lm -lz -L.. -lbam -lpthread
+		$(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
 
 bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
 		$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
diff --git a/misc/bamcheck.c b/misc/bamcheck.c
index 532d105..352db21 100644
--- a/misc/bamcheck.c
+++ b/misc/bamcheck.c
@@ -116,15 +116,18 @@ typedef struct
     uint64_t total_len_dup;
     uint64_t nreads_1st;
     uint64_t nreads_2nd;
+    uint64_t nreads_filtered;
     uint64_t nreads_dup;
     uint64_t nreads_unmapped;
     uint64_t nreads_unpaired;
     uint64_t nreads_paired;
+    uint64_t nreads_anomalous;
     uint64_t nreads_mq0;
     uint64_t nbases_mapped;
     uint64_t nbases_mapped_cigar;
     uint64_t nbases_trimmed;  // bwa trimmed bases
     uint64_t nmismatches;
+    uint64_t nreads_QCfailed, nreads_secondary;
 
     // GC-depth related data
     uint32_t ngcd, igcd;        // The maximum number of GC depth bins and index of the current bin
@@ -395,7 +398,7 @@ void count_mismatches_per_cycle(stats_t *stats,bam1_t *bam_line)
             {
                 uint8_t qual = quals[iread] + 1;
                 if ( qual>=stats->nquals )
-                    error("TODO: quality too high %d>=%d\n", quals[iread],stats->nquals);
+                    error("TODO: quality too high %d>=%d (%s %d %s)\n", qual,stats->nquals, stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1,bam1_qname(bam_line));
 
                 int idx = is_fwd ? icycle : read_len-icycle-1;
                 if ( idx>stats->max_len )
@@ -515,9 +518,9 @@ void realloc_gcd_buffer(stats_t *stats, int seq_len)
 
     int n = 1 + stats->gcd_ref_size / (stats->gcd_bin_size - seq_len);
     if ( n <= stats->igcd )
-        error("Uh: n=%d igcd=%d\n", n,stats->igcd );
+        error("The --GC-depth bin size is too small or reference genome too big; please decrease the bin size or increase the reference length\n");
         
-    if ( n >= stats->ngcd )
+    if ( n > stats->ngcd )
     {
         stats->gcd = realloc(stats->gcd, n*sizeof(gc_depth_t));
         if ( !stats->gcd )
@@ -617,16 +620,26 @@ void collect_stats(bam1_t *bam_line, stats_t *stats)
         if ( k == kh_end(stats->rg_hash) ) return;
     }
     if ( stats->flag_require && (bam_line->core.flag & stats->flag_require)!=stats->flag_require )
+    {
+        stats->nreads_filtered++;
         return;
+    }
     if ( stats->flag_filter && (bam_line->core.flag & stats->flag_filter) )
+    {
+        stats->nreads_filtered++;
         return;
-
+    }
     if ( !is_in_regions(bam_line,stats) )
         return;
+    if ( stats->filter_readlen!=-1 && bam_line->core.l_qseq!=stats->filter_readlen ) 
+        return;
+
+    if ( bam_line->core.flag & BAM_FQCFAIL ) stats->nreads_QCfailed++;
+    if ( bam_line->core.flag & BAM_FSECONDARY ) stats->nreads_secondary++;
 
     int seq_len = bam_line->core.l_qseq;
     if ( !seq_len ) return;
-    if ( stats->filter_readlen!=-1 && seq_len!=stats->filter_readlen ) return;
+
     if ( seq_len >= stats->nbases )
         realloc_buffers(stats,seq_len);
     if ( stats->max_len<seq_len )
@@ -684,7 +697,7 @@ void collect_stats(bam1_t *bam_line, stats_t *stats)
     {
         uint8_t qual = bam_quals[ reverse ? seq_len-i-1 : i];
         if ( qual>=stats->nquals )
-            error("TODO: quality too high %d>=%d\n", quals[i],stats->nquals);
+            error("TODO: quality too high %d>=%d (%s %d %s)\n", qual,stats->nquals,stats->sam->header->target_name[bam_line->core.tid],bam_line->core.pos+1,bam1_qname(bam_line));
         if ( qual>stats->max_qual )
             stats->max_qual = qual;
 
@@ -702,42 +715,48 @@ void collect_stats(bam1_t *bam_line, stats_t *stats)
 
         count_indels(stats,bam_line);
 
-        // The insert size is tricky, because for long inserts the libraries are
-        // prepared differently and the pairs point in other direction. BWA does
-        // not set the paired flag for them.  Similar thing is true also for 454
-        // reads. Therefore, do the insert size stats for all mapped reads.
-        int32_t isize = bam_line->core.isize;
-        if ( isize<0 ) isize = -isize;
-        if ( IS_PAIRED(bam_line) && isize!=0 )
+        if ( !IS_PAIRED(bam_line) )
+            stats->nreads_unpaired++;
+        else 
         {
             stats->nreads_paired++;
-            if ( isize >= stats->nisize )
-                isize=stats->nisize-1;
 
-            int pos_fst = bam_line->core.mpos - bam_line->core.pos;
-            int is_fst  = IS_READ1(bam_line) ? 1 : -1;
-            int is_fwd  = IS_REVERSE(bam_line) ? -1 : 1;
-            int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1;
+            if ( bam_line->core.tid!=bam_line->core.mtid )
+                stats->nreads_anomalous++;
 
-            if ( is_fwd*is_mfwd>0 )
-                stats->isize_other[isize]++;
-            else if ( is_fst*pos_fst>0 )
-            {
-                if ( is_fst*is_fwd>0 )
-                    stats->isize_inward[isize]++;
-                else
-                    stats->isize_outward[isize]++;
-            }
-            else if ( is_fst*pos_fst<0 )
+            // The insert size is tricky, because for long inserts the libraries are
+            // prepared differently and the pairs point in other direction. BWA does
+            // not set the paired flag for them.  Similar thing is true also for 454
+            // reads. Mates mapped to different chromosomes have isize==0.
+            int32_t isize = bam_line->core.isize;
+            if ( isize<0 ) isize = -isize;
+            if ( isize >= stats->nisize )
+                isize = stats->nisize-1;
+            if ( isize>0 || bam_line->core.tid==bam_line->core.mtid )
             {
-                if ( is_fst*is_fwd>0 )
-                    stats->isize_outward[isize]++;
-                else
-                    stats->isize_inward[isize]++;
+                int pos_fst = bam_line->core.mpos - bam_line->core.pos;
+                int is_fst  = IS_READ1(bam_line) ? 1 : -1;
+                int is_fwd  = IS_REVERSE(bam_line) ? -1 : 1;
+                int is_mfwd = IS_MATE_REVERSE(bam_line) ? -1 : 1;
+
+                if ( is_fwd*is_mfwd>0 )
+                    stats->isize_other[isize]++;
+                else if ( is_fst*pos_fst>0 )
+                {
+                    if ( is_fst*is_fwd>0 )
+                        stats->isize_inward[isize]++;
+                    else
+                        stats->isize_outward[isize]++;
+                }
+                else if ( is_fst*pos_fst<0 )
+                {
+                    if ( is_fst*is_fwd>0 )
+                        stats->isize_outward[isize]++;
+                    else
+                        stats->isize_inward[isize]++;
+                }
             }
         }
-        else
-            stats->nreads_unpaired++;
 
         // Number of mismatches 
         uint8_t *nm = bam_aux_get(bam_line,"NM");
@@ -889,7 +908,7 @@ void output_stats(stats_t *stats)
     // Calculate average insert size and standard deviation (from the main bulk data only)
     int isize, ibulk=0;
     uint64_t nisize=0, nisize_inward=0, nisize_outward=0, nisize_other=0;
-    for (isize=1; isize<stats->nisize; isize++)
+    for (isize=0; isize<stats->nisize; isize++)
     {
         // Each pair was counted twice
         stats->isize_inward[isize] *= 0.5;
@@ -903,7 +922,7 @@ void output_stats(stats_t *stats)
     }
 
     double bulk=0, avg_isize=0, sd_isize=0;
-    for (isize=1; isize<stats->nisize; isize++)
+    for (isize=0; isize<stats->nisize; isize++)
     {
         bulk += stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize];
         avg_isize += isize * (stats->isize_inward[isize] + stats->isize_outward[isize] + stats->isize_other[isize]);
@@ -928,6 +947,8 @@ void output_stats(stats_t *stats)
         printf(" %s",stats->argv[i]);
     printf("\n");
     printf("# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n");
+    printf("SN\traw total sequences:\t%ld\n", (long)(stats->nreads_filtered+stats->nreads_1st+stats->nreads_2nd));
+    printf("SN\tfiltered sequences:\t%ld\n", (long)stats->nreads_filtered);
     printf("SN\tsequences:\t%ld\n", (long)(stats->nreads_1st+stats->nreads_2nd));
     printf("SN\tis paired:\t%d\n", stats->nreads_1st&&stats->nreads_2nd ? 1 : 0);
     printf("SN\tis sorted:\t%d\n", stats->is_sorted ? 1 : 0);
@@ -939,6 +960,8 @@ void output_stats(stats_t *stats)
     printf("SN\treads paired:\t%ld\n", (long)stats->nreads_paired);
     printf("SN\treads duplicated:\t%ld\n", (long)stats->nreads_dup);
     printf("SN\treads MQ0:\t%ld\n", (long)stats->nreads_mq0);
+    printf("SN\treads QC failed:\t%ld\n", (long)stats->nreads_QCfailed);
+    printf("SN\tnon-primary alignments:\t%ld\n", (long)stats->nreads_secondary);
     printf("SN\ttotal length:\t%ld\n", (long)stats->total_len);
     printf("SN\tbases mapped:\t%ld\n", (long)stats->nbases_mapped);
     printf("SN\tbases mapped (cigar):\t%ld\n", (long)stats->nbases_mapped_cigar);
@@ -955,6 +978,7 @@ void output_stats(stats_t *stats)
     printf("SN\tinward oriented pairs:\t%ld\n", (long)nisize_inward);
     printf("SN\toutward oriented pairs:\t%ld\n", (long)nisize_outward);
     printf("SN\tpairs with other orientation:\t%ld\n", (long)nisize_other);
+    printf("SN\tpairs on different chromosomes:\t%ld\n", (long)stats->nreads_anomalous/2);
 
     int ibase,iqual;
     if ( stats->max_len<stats->nbases ) stats->max_len++;
@@ -1021,7 +1045,7 @@ void output_stats(stats_t *stats)
         printf("GCC\t%d\t%.2f\t%.2f\t%.2f\t%.2f\n", ibase,100.*ptr[0]/sum,100.*ptr[1]/sum,100.*ptr[2]/sum,100.*ptr[3]/sum);
     }
     printf("# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: pairs total, inward oriented pairs, outward oriented pairs, other pairs\n");
-    for (isize=1; isize<ibulk; isize++)
+    for (isize=0; isize<ibulk; isize++)
         printf("IS\t%d\t%ld\t%ld\t%ld\t%ld\n", isize, (long)(stats->isize_inward[isize]+stats->isize_outward[isize]+stats->isize_other[isize]),
             (long)stats->isize_inward[isize], (long)stats->isize_outward[isize], (long)stats->isize_other[isize]);
 
@@ -1050,12 +1074,14 @@ void output_stats(stats_t *stats)
     }
 
     printf("# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.\n");
-    printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
+    if  ( stats->cov[0] )
+        printf("COV\t[<%d]\t%d\t%ld\n",stats->cov_min,stats->cov_min-1, (long)stats->cov[0]);
     int icov;
     for (icov=1; icov<stats->ncov-1; icov++)
-        printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
-    printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
-
+        if ( stats->cov[icov] )
+            printf("COV\t[%d-%d]\t%d\t%ld\n",stats->cov_min + (icov-1)*stats->cov_step, stats->cov_min + icov*stats->cov_step-1,stats->cov_min + icov*stats->cov_step-1, (long)stats->cov[icov]);
+    if ( stats->cov[stats->ncov-1] )
+        printf("COV\t[%d<]\t%d\t%ld\n",stats->cov_min + (stats->ncov-2)*stats->cov_step-1,stats->cov_min + (stats->ncov-2)*stats->cov_step-1, (long)stats->cov[stats->ncov-1]);
 
     // Calculate average GC content, then sort by GC and depth
     printf("# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n");
@@ -1279,7 +1305,7 @@ void error(const char *format, ...)
         printf("    -d, --remove-dups                   Exlude from statistics reads marked as duplicates\n");
         printf("    -f, --required-flag <int>           Required flag, 0 for unset [0]\n");
         printf("    -F, --filtering-flag <int>          Filtering flag, 0 for unset [0]\n");
-        printf("        --GC-depth <float,float>        Bin size for GC-depth graph and the maximum reference length [2e4,6e9]\n");
+        printf("        --GC-depth <float,float>        Bin size for GC-depth graph and the maximum reference length [2e4,4.2e9]\n");
         printf("    -h, --help                          This help message\n");
         printf("    -i, --insert-size <int>             Maximum insert size [8000]\n");
         printf("    -I, --id <string>                   Include only listed read group or sample name\n");
@@ -1311,16 +1337,17 @@ int main(int argc, char *argv[])
 
     stats_t *stats = calloc(1,sizeof(stats_t));
     stats->ngc    = 200;
-    stats->nquals = 95;
+    stats->nquals = 256;
     stats->nbases = 300;
     stats->nisize = 8000;
     stats->max_len   = 30;
     stats->max_qual  = 40;
     stats->isize_main_bulk = 0.99;   // There are always outliers at the far end
     stats->gcd_bin_size = 20e3;
-    stats->gcd_ref_size = 3e9;
+    stats->gcd_ref_size = 4.2e9;
     stats->rseq_pos     = -1;
-    stats->tid = stats->gcd_pos = stats->igcd = -1;
+    stats->tid = stats->gcd_pos = -1;
+    stats->igcd = 0;
     stats->is_sorted = 1;
     stats->cov_min  = 1;
     stats->cov_max  = 1000;
diff --git a/sam_header.c b/sam_header.c
index a1b5181..ddc2c38 100644
--- a/sam_header.c
+++ b/sam_header.c
@@ -366,6 +366,7 @@ static HeaderLine *sam_header_line_parse(const char *headerLine)
     while (*to && *to=='\t') to++;
     if ( to-from != 1 ) {
         debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+        free(hline);
 		return 0;
 	}
     from = to;
diff --git a/samtools.1 b/samtools.1
index 4b3f75a..869feaa 100644
--- a/samtools.1
+++ b/samtools.1
@@ -353,7 +353,7 @@ which enables fast BAM concatenation.
 
 .TP
 .B sort
-samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+samtools sort [-nof] [-m maxMem] <in.bam> <out.prefix>
 
 Sort alignments by leftmost coordinates. File
 .I <out.prefix>.bam
@@ -371,6 +371,13 @@ Output the final alignment to the standard output.
 .B -n
 Sort by read names rather than by chromosomal coordinates
 .TP
+.B -f
+Use
+.I <out.prefix>
+as the full output path and do not append
+.I .bam
+suffix.
+.TP
 .BI -m \ INT
 Approximately the maximum required memory. [500000000]
 .RE