boolean read_event_definitions (char *filename)
{
char tmpbuf [128];
initialize_events();
s_elog_hfp = fopen (filename, "rt");
if (s_elog_hfp == NULL) {
sprintf (tmpbuf, "Couldn't open %s\n", filename);
infobox ("Open Failed", tmpbuf);
return(FALSE);
}
/* Presume "elog.h". Note fallthrough... */
if (read_header_files()) {
sort_event_definitions();
create_point_selector();
recompute_ps_vscrollbar();
fclose(s_elog_hfp);
view1_display_when_idle();
remove_needed = TRUE;
return(TRUE);
}
fclose(s_elog_hfp);
s_hfp = fopen (filename, "rt");
if (s_hfp == NULL) {
sprintf (tmpbuf, "Couldn't open %s\n", filename);
infobox ("Read Event Definition Failure", tmpbuf);
return(FALSE);
}
read_header_file();
/* Happens if the user feeds us the wrong file, for example */
if (g_neventdefs == 0) {
sprintf (tmpbuf, "No event definitions found in %s\n", filename);
infobox ("No Event Definitions?", tmpbuf);
return(FALSE);
}
finalize_events();
return(TRUE);
}
int do_map_header(char *date)
{
char temp[100];
/* set color and font */
set_ps_color(&hdr.color);
fontsize = (double)hdr.fontsize;
fprintf(PS.fp, "(%s) FN %.1f SF\n", hdr.font, fontsize);
/* set start of first line */
dy = 1.2 * fontsize;
y = 72.0 * (PS.page_height - PS.top_marg) - fontsize - 1.5;
if (hdr.fp == NULL) {
if (PS.celltitle[0]) {
fprintf(PS.fp, "/t (TITLE: %s) def\n", PS.celltitle);
fprintf(PS.fp, "t SW pop %.1f XS D2 t exch %.1f MS\n",
72 * PS.page_width, y);
y -= dy;
}
strcpy(temp, G_myname());
G_strip(temp);
if (*temp == 0)
strcpy(temp, G_location());
fprintf(PS.fp, "/t (LOCATION: %s) def\n", temp);
fprintf(PS.fp, "t SW pop %.1f XS D2 t exch %.1f MS\n",
72 * PS.page_width, y);
y -= 0.25 * dy;
if (PS.min_y > y)
PS.min_y = y;
return 0;
}
x = 72.0 * PS.left_marg + 1.5;
read_header_file(date);
y -= 0.25 * dy;
if (PS.min_y > y)
PS.min_y = y;
return 0;
}
static void reheader_vcf(args_t *args)
{
kstring_t hdr = {0,0,0};
htsFile *fp = hts_open(args->fname, "r"); if ( !fp ) error("Failed to open: %s\n", args->fname);
while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 )
{
kputc('\n',&fp->line); // hts_getline eats the newline character
if ( fp->line.s[0]!='#' ) break;
kputsn(fp->line.s,fp->line.l,&hdr);
}
int nsamples = 0;
char **samples = NULL;
if ( args->samples_fname )
samples = hts_readlines(args->samples_fname, &nsamples);
if ( args->header_fname )
{
free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
read_header_file(args->header_fname, &hdr);
}
if ( samples )
{
set_samples(samples, nsamples, &hdr);
int i;
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
}
int out = STDOUT_FILENO;
if ( write(out, hdr.s, hdr.l)!=hdr.l ) error("Failed to write %d bytes\n", hdr.l);
free(hdr.s);
if ( fp->line.l )
{
if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %d bytes\n", fp->line.l);
}
while ( hts_getline(fp, KS_SEP_LINE, &fp->line) >=0 ) // uncompressed file implies small size, we don't worry about speed
{
kputc('\n',&fp->line);
if ( write(out, fp->line.s, fp->line.l)!=fp->line.l ) error("Failed to write %d bytes\n", fp->line.l);
}
hts_close(fp);
}
static boolean read_header_files (void)
{
char *cp, *name;
char tmpbuf [1024];
int basenum;
boolean rv=FALSE;
while (fgets (tmpbuf, sizeof (tmpbuf), s_elog_hfp))
{
cp = tmpbuf;
if (strncmp (cp, "#define", 7))
continue;
cp += 7;
/* skip ws after #define */
while (*cp && isspace ((int)*cp))
cp++;
if (*cp == 0)
continue;
/* skip EV_COMPxxx_START */
while (*cp && !isspace((int)*cp))
cp++;
if (*cp == 0)
continue;
/* skip ws after EV_COMPxxx_START */
while (*cp && isspace ((int)*cp))
cp++;
if (*cp == 0)
continue;
basenum = atol (cp);
/* skip #define */
while (*cp && (*cp != '/'))
cp++;
if (*cp == 0)
continue;
cp++;
if (*cp != '*')
continue;
cp++;
/* skip ws after comment start */
while (*cp && isspace ((int)*cp))
cp++;
if (*cp == 0)
continue;
if (strncmp (cp, "pointdefs:", 10))
continue;
cp += 10;
/* skip ws after comment start */
while (*cp && isspace ((int)*cp))
cp++;
name = cp;
while (*cp && !isspace ((int)*cp))
cp++;
*cp = 0;
s_hfp = fopen (name, "rt");
if (s_hfp == NULL) {
g_warning ("Couldn't open header file %s\n", name);
continue;
}
rv = TRUE;
s_basenum = basenum;
read_header_file();
fclose (s_hfp);
}
return(rv);
}
static void reheader_bcf(args_t *args, int is_compressed)
{
htsFile *fp = hts_open(args->fname, "r"); if ( !fp ) error("Failed to open: %s\n", args->fname);
bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname);
kstring_t htxt = {0,0,0};
int hlen;
htxt.s = bcf_hdr_fmt_text(hdr, 1, &hlen);
htxt.l = hlen;
int i, nsamples = 0;
char **samples = NULL;
if ( args->samples_fname )
samples = hts_readlines(args->samples_fname, &nsamples);
if ( args->header_fname )
{
free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0;
read_header_file(args->header_fname, &htxt);
}
if ( samples )
{
set_samples(samples, nsamples, &htxt);
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
}
bcf_hdr_t *hdr_out = bcf_hdr_init("r");
bcf_hdr_parse(hdr_out, htxt.s);
if ( args->header_fname ) hdr_out = strip_header(hdr, hdr_out);
// write the header and the body
htsFile *fp_out = hts_open("-",is_compressed ? "wb" : "wbu");
bcf_hdr_write(fp_out, hdr_out);
bcf1_t *rec = bcf_init();
while ( bcf_read(fp, hdr, rec)==0 )
{
// sanity checking, this slows things down. Make it optional?
bcf_unpack(rec, BCF_UN_ALL);
if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) )
error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid));
for (i=0; i<rec->d.n_flt; i++)
{
int id = rec->d.flt[i];
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->d.n_flt )
error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i]));
for (i=0; i<rec->n_info; i++)
{
int id = rec->d.info[i].key;
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->n_info )
error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key));
for (i=0; i<rec->n_fmt; i++)
{
int id = rec->d.fmt[i].id;
if ( id >= hdr_out->n[BCF_DT_ID] ) break;
if ( !hdr_out->id[BCF_DT_ID][id].key ) break;
if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break;
if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) )
error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key);
}
if ( i!=rec->n_fmt )
error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id));
bcf_write(fp_out,hdr_out,rec);
}
bcf_destroy(rec);
free(htxt.s);
hts_close(fp_out);
hts_close(fp);
bcf_hdr_destroy(hdr_out);
bcf_hdr_destroy(hdr);
}
static void reheader_vcf_gz(args_t *args)
{
BGZF *fp = bgzf_open(args->fname,"r");
if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
error("Failed to read %s: %s\n", args->fname, strerror(errno));
kstring_t hdr = {0,0,0};
char *buffer = (char*) fp->uncompressed_block;
// Read the header and find the position of the data block
if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]);
int skip_until = 1; // end of the header in the current uncompressed block
while (1)
{
if ( buffer[skip_until]=='\n' )
{
skip_until++;
if ( skip_until>=fp->block_length )
{
kputsn(buffer,skip_until,&hdr);
if ( bgzf_read_block(fp) != 0 || !fp->block_length ) error("FIXME: No body in the file: %s\n", args->fname);
skip_until = 0;
}
// The header has finished
if ( buffer[skip_until]!='#' )
{
kputsn(buffer,skip_until,&hdr);
break;
}
}
skip_until++;
if ( skip_until>=fp->block_length )
{
kputsn(buffer,fp->block_length,&hdr);
if (bgzf_read_block(fp) != 0 || !fp->block_length) error("FIXME: No body in the file: %s\n", args->fname);
skip_until = 0;
}
}
int nsamples = 0;
char **samples = NULL;
if ( args->samples_fname )
samples = hts_readlines(args->samples_fname, &nsamples);
if ( args->header_fname )
{
free(hdr.s); hdr.s = NULL; hdr.l = hdr.m = 0;
read_header_file(args->header_fname, &hdr);
}
if ( samples )
{
set_samples(samples, nsamples, &hdr);
int i;
for (i=0; i<nsamples; i++) free(samples[i]);
free(samples);
}
// Output the modified header
BGZF *bgzf_out = bgzf_dopen(fileno(stdout), "w");
bgzf_write(bgzf_out, hdr.s, hdr.l);
free(hdr.s);
// Output all remainig data read with the header block
if ( fp->block_length - skip_until > 0 )
{
if ( bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until)<0 ) error("Error: %d\n",fp->errcode);
}
if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode);
// Stream the rest of the file without as it is, without decompressing
ssize_t nread;
int page_size = getpagesize();
char *buf = (char*) valloc(page_size);
while (1)
{
nread = bgzf_raw_read(fp, buf, page_size);
if ( nread<=0 ) break;
int count = bgzf_raw_write(bgzf_out, buf, nread);
if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
}
if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
if (bgzf_close(fp) < 0) error("Error: %d\n",fp->errcode);
free(buf);
}
tan_t* tan_read_header_file_ext_only(const char* fn, int ext, tan_t* dest) {
return read_header_file(fn, ext, TRUE, dest, call_tan_read_header);
}
tan_t* tan_read_header_file_ext(const char* fn, int ext, tan_t* dest) {
return read_header_file(fn, ext, FALSE, dest, call_tan_read_header);
}
tan_t* tan_read_header_file(const char* fn, tan_t* dest) {
return read_header_file(fn, 0, FALSE, dest, call_tan_read_header);
}
sip_t* sip_read_header_file_ext_only(const char* fn, int ext, sip_t* dest) {
return read_header_file(fn, ext, TRUE, dest, call_sip_read_header);
}
sip_t* sip_read_header_file(const char* fn, sip_t* dest) {
return read_header_file(fn, 0, FALSE, dest, call_sip_read_header);
}
