void make_format(int gno)
{
int type, locpx, locfx, locpy, locfy;
type = g[gno].pt_type;
locfx = get_format_index(g[gno].fx);
locfy = get_format_index(g[gno].fy);
locpx = g[gno].px;
locpy = g[gno].py;
switch (type) {
case 0:
if (locfx < 3 && locfy < 3) {
sprintf(locator_format, "G%%1d: %s = [%%.%d%s, %%.%d%s]",
typestr[type], locpx, fchar[locfx], locpy, fchar[locfy]);
} else {
locator_format[0] = 0;
}
break;
case 2:
locfx = locfx == FORMAT_DECIMAL ? 0 :
locfx == FORMAT_EXPONENTIAL ? 1 :
locfx == FORMAT_GENERAL ? 2 : 0;
sprintf(locator_format, "G%%1d: %s = [%%.%d%s]", typestr[type], locpx,
fchar[locfx]);
break;
case 1:
case 3:
case 4:
locfx = locfx == FORMAT_DECIMAL ? 0 :
locfx == FORMAT_EXPONENTIAL ? 1 :
locfx == FORMAT_GENERAL ? 2 : 0;
locfy = locfy == FORMAT_DECIMAL ? 0 :
locfy == FORMAT_EXPONENTIAL ? 1 :
locfy == FORMAT_GENERAL ? 2 : 0;
sprintf(locator_format, "G%%1d: %s = [%%.%d%s, %%.%d%s]", typestr[type],
locpx, fchar[locfx], locpy, fchar[locfy]);
break;
case 5:
sprintf(locator_format, "G%%1d: %s = [%%d, %%d]", typestr[type]);
break;
}
}
void vcf_parse_geno_probs(VCFInfo *vcf_info, float *geno_probs, char *cur) {
long gl_idx, gp_idx;
/* get index of GP and GL tokens in format string */
gp_idx = get_format_index(vcf_info->format, "GP");
gl_idx = get_format_index(vcf_info->format, "GL");
if((gl_idx == -1) && (gp_idx == -1)) {
my_err("%s:%d: VCF format string does not specify GL or GP token "
"so cannot obtain genotype probabilities. Format string: '%s'.\n"
"To use this file, you must run snp2h5 without "
"the --geno_prob option.", __FILE__, __LINE__,
vcf_info->format);
}
if(gp_idx > -1) {
vcf_parse_gp(vcf_info, geno_probs, cur, gp_idx);
return;
}
vcf_parse_gl(vcf_info, geno_probs, cur, gl_idx);
}
static int get_format(char *type, char buf[5])
{
int i;
const char types[][24] = {
"char", "unsigned char", "short", "unsigned short",
"int", "unsigned int", "long long int", "unsigned long long int",
"void*", "char*", "float", "double", "long double", "size_t", "t_byte",
""};
i = 0;
while (*types[i] != '\0' && !ft_strequ(types[i], type))
i++;
if (types[i] == NULL)
return (0);
get_format_index(i, buf);
return (i);
}
static void update_ticklabel_items(int gno)
{
Arg a;
tickmarks t;
int iv;
if (ticklabel_frame) {
get_graph_tickmarks(gno, &t, curaxis);
SetChoice(tlfont, t.tl_font);
SetChoice(tlcolor, t.tl_color);
SetChoice(tllinew, t.tl_linew - 1);
SetChoice(tlskip, t.tl_skip);
SetChoice(tlstagger, t.tl_staggered);
xv_setstr(tlappstr, t.tl_appstr);
xv_setstr(tlprestr, t.tl_prestr);
SetChoice(tlstarttype, t.tl_starttype == TYPE_SPEC);
if (t.tl_starttype == TYPE_SPEC) {
sprintf(buf, "%f", t.tl_start);
xv_setstr(tlstart, buf);
sprintf(buf, "%f", t.tl_stop);
xv_setstr(tlstop, buf);
}
SetChoice(tlstoptype, t.tl_stoptype == TYPE_SPEC);
if (t.tl_stoptype == TYPE_SPEC) {
sprintf(buf, "%f", t.tl_stop);
xv_setstr(tlstop, buf);
}
iv = get_format_index(t.tl_format);
SetChoice(tlform, iv);
switch (t.tl_op) {
case PLACE_LEFT:
SetChoice(ticklop, 0);
break;
case PLACE_RIGHT:
SetChoice(ticklop, 1);
break;
case PLACE_BOTTOM:
SetChoice(ticklop, 0);
break;
case PLACE_TOP:
SetChoice(ticklop, 1);
break;
case PLACE_BOTH:
SetChoice(ticklop, 2);
break;
}
switch (t.tl_sign) {
case SIGN_NORMAL:
SetChoice(tlsign, 0);
break;
case SIGN_ABSOLUTE:
SetChoice(tlsign, 1);
break;
case SIGN_NEGATE:
SetChoice(tlsign, 2);
break;
}
SetChoice(tlprec, t.tl_prec);
iv = (int) (100 * t.tl_charsize);
XtSetArg(a, XmNvalue, iv);
XtSetValues(tlcharsize, &a, 1);
switch (t.tl_layout) {
case TICKS_HORIZONTAL:
SetChoice(tllayout, 0);
break;
case TICKS_VERTICAL:
SetChoice(tllayout, 1);
break;
case TYPE_SPEC:
SetChoice(tllayout, 2);
break;
}
switch (t.tl_loc) {
case LABEL_ONTICK:
SetChoice(tlloc, 0);
break;
case LABEL_BETWEEN:
SetChoice(tlloc, 1);
break;
}
iv = (int) t.tl_angle % 360;
XtSetArg(a, XmNvalue, iv);
XtSetValues(tlangle, &a, 1);
}
}
void vcf_parse_haplotypes(VCFInfo *vcf_info, char *haplotypes,
char *cur) {
int gt_idx, hap1, hap2, i, n;
static int warn_phase = TRUE;
static int warn_parse = TRUE;
long expect_haps, n_haps;
char gt_str[VCF_MAX_FORMAT];
/* char delim[] = " \t"; */
char delim[] = "\t";
char inner_delim[] = ":";
char *inner_cur, *tok, *inner_tok;
/* get index of GT token in format string*/
gt_idx = get_format_index(vcf_info->format, "GT");
if(gt_idx == -1) {
my_err("%s:%d: VCF format string does not specify GT token "
"so cannot obtain haplotypes. Format string: '%s'.\n"
"To use this file, you must run snp2h5 without "
"the --haplotype option.",
__FILE__, __LINE__, vcf_info->format);
}
expect_haps = vcf_info->n_sample * 2;
n_haps = 0;
while((tok = strsep(&cur, delim)) != NULL) {
/* Each genotype string is delimited by ':'
* The GT portions of the string are delimited by '/' or '|'
* '|' indicates phased, '/' indicates unphased.
*/
util_strncpy(gt_str, tok, sizeof(gt_str));
i = 0;
inner_cur = gt_str;
while((i <= gt_idx) && (inner_tok = strsep(&inner_cur, inner_delim)) != NULL) {
if(i == gt_idx) {
n = sscanf(inner_tok, "%d|%d", &hap1, &hap2);
if(n != 2) {
/* try with '/' separator instead */
n = sscanf(inner_tok, "%d/%d", &hap1, &hap2);
if(n == 2) {
if(warn_phase) {
my_warn("%s:%d: some genotypes are unphased (delimited "
"with '/' instead of '|')\n", __FILE__, __LINE__,
inner_tok);
warn_phase = FALSE;
}
} else {
if(warn_parse) {
my_warn("%s:%d: could not parse some genotype "
"strings that look like: '%s'\n", __FILE__, __LINE__,
inner_tok);
warn_parse = FALSE;
}
hap1 = VCF_GTYPE_MISSING;
hap2 = VCF_GTYPE_MISSING;
}
}
if((hap1 != VCF_GTYPE_MISSING && hap1 != 0 && hap1 != 1) ||
(hap2 != VCF_GTYPE_MISSING && hap2 != 0 && hap2 != 1)) {
/* Copy number polymorphisms and multi-allelic SNPs
* can have values other than 0 and 1 (e.g. 3, 4, ...).
* Combined haplotype test does not currently deal with
* these. Set the genotypes to MISSING (-1)
*/
hap1 = VCF_GTYPE_MISSING;
hap2 = VCF_GTYPE_MISSING;
}
if((n_haps + 2) > expect_haps) {
my_err("%s:%d: more genotypes per line than expected",
__FILE__, __LINE__);
}
haplotypes[n_haps] = hap1;
haplotypes[n_haps+1] = hap2;
n_haps += 2;
}
i++;
}
}
if(n_haps != expect_haps) {
my_err("%s:%d: expected %ld genotype values per line, but got "
"%ld", __FILE__, __LINE__, expect_haps, n_haps);
}
}
