int gt_reverse_complement(char *dna_seq, unsigned long seqlen, GtError *err)
{
char *front_char, *back_char, tmp_char;
int had_err = 0;
gt_error_check(err);
gt_assert(dna_seq);
for (front_char = dna_seq, back_char = dna_seq + seqlen - 1;
front_char <= back_char;
front_char++, back_char--) {
had_err = gt_complement(&tmp_char, *front_char, err);
if (!had_err)
had_err = gt_complement(front_char, *back_char, err);
if (!had_err)
*back_char = tmp_char;
if (had_err)
break;
}
return had_err;
}
static int snp_annotator_visitor_feature_node(GtNodeVisitor *nv,
GtFeatureNode *fn,
GtError *err)
{
int had_err = 0;
GtSNPAnnotatorVisitor *sav;
GtFeatureNodeIterator *fni,
*mrnafni;
GtFeatureNode *curnode,
*curnode2;
GtRange snp_rng;
gt_error_check(err);
sav = snp_annotator_visitor_cast(nv);
/* ignore non-nodes */
if (!fn) return 0;
/* only process SNPs */
if (!(gt_feature_node_get_type(fn) == sav->SNV_type ||
gt_feature_node_get_type(fn) == sav->SNP_type)) {
return 0;
}
fni = gt_feature_node_iterator_new_direct(sav->gene);
snp_rng = gt_genome_node_get_range((GtGenomeNode*) fn);
while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) {
if (gt_feature_node_get_type(curnode) == sav->mRNA_type) {
GtStrand mrna_strand = gt_feature_node_get_strand(curnode);
#ifndef NDEBUG
const char *refstr;
#endif
GtUword mrnasnppos = 0;
mrnafni = gt_feature_node_iterator_new(curnode);
while (!had_err && (curnode2 = gt_feature_node_iterator_next(mrnafni))) {
if (gt_feature_node_get_type(curnode2) == sav->CDS_type) {
GtRange cds_rng = gt_genome_node_get_range((GtGenomeNode*) curnode2);
if (gt_range_overlap(&snp_rng, &cds_rng)) {
char *mRNA,
origchar;
char *variantchars, *variantptr = NULL;
GT_UNUSED char *refchars, *refptr = NULL;
mRNA = (char*) gt_hashmap_get(sav->rnaseqs, curnode);
gt_assert(mRNA);
gt_assert(snp_rng.start >= cds_rng.start);
mrnasnppos += (snp_rng.start - cds_rng.start);
if (mrna_strand == GT_STRAND_REVERSE)
mrnasnppos = strlen(mRNA) - mrnasnppos - 1;
gt_assert(mrnasnppos < strlen(mRNA));
origchar = mRNA[mrnasnppos];
#ifndef NDEBUG
refstr = refptr = gt_cstr_dup(gt_feature_node_get_attribute(fn,
GT_GVF_REFERENCE_SEQ));
if (!had_err && refstr) {
if (gt_feature_node_get_strand(curnode) == GT_STRAND_REVERSE) {
int rval = gt_complement(&origchar, origchar, err);
gt_assert(rval == 0);
}
gt_assert(toupper(origchar) == toupper(refstr[0]));
}
#endif
variantchars = variantptr = gt_cstr_dup(
gt_feature_node_get_attribute(fn, GT_GVF_VARIANT_SEQ));
if (!had_err && variantchars) {
GtUword i = 0;
while (!had_err &&
(*variantchars != ';' && *variantchars != '\0')) {
if (*variantchars != ',' && *variantchars != origchar) {
char variantchar = *variantchars;
#ifndef NDEBUG
char refchar = refstr ? refstr[0] : '-'; /* XXX */
if (!had_err && mrna_strand == GT_STRAND_REVERSE)
had_err = gt_complement(&refchar, refchar, err);
#endif
if (!had_err && mrna_strand == GT_STRAND_REVERSE)
had_err = gt_complement(&variantchar, variantchar, err);
if (!had_err) {
had_err = snp_annotator_classify_snp(sav, curnode, fn,
mrnasnppos,
i++,
variantchar,
#ifndef NDEBUG
refchar,
#endif
err);
}
} else if (*variantchars == origchar) {
i++;
}
variantchars++;
}
gt_free(variantptr);
gt_free(refptr);
}
} else {
mrnasnppos += gt_range_length(&cds_rng);
}
}
}
gt_feature_node_iterator_delete(mrnafni);
}
}
gt_feature_node_iterator_delete(fni);
return had_err;
}
static void gt_hpol_processor_output_stats(GtAlignedSegment *as,
unsigned long r_hpos, unsigned long coverage, unsigned long r_hlen,
unsigned long r_supp, unsigned long s_hlen, unsigned long a_hlen,
unsigned long a_supp, char s_char, double s_q_ave,
unsigned long c_len, GtFile *outfp)
{
unsigned long i, pos, s_hpos = 0, s_offset, s_q_bef, s_q_aft, s_q_value,
s_q_min, s_q_max, s_q_range, s_q_first, s_q_last = 0, s_hend,
s_mapq;
char *s_qual, *q, edit, s_or;
const char *s_id;
gt_assert(r_hlen != s_hlen);
edit = r_hlen > s_hlen ? 'I' : 'D';
gt_assert(coverage > 0);
r_supp = r_supp * 100 / coverage;
a_supp = a_supp * 100 / coverage;
s_id = gt_aligned_segment_description(as);
s_mapq = gt_aligned_segment_mapping_quality(as);
q = gt_aligned_segment_qual(as);
gt_assert(s_hlen > 0);
s_hpos = gt_aligned_segment_orig_seqpos_for_refpos(as, r_hpos);
s_offset = gt_aligned_segment_offset_for_refpos(as, r_hpos);
s_qual = gt_malloc(sizeof (*s_qual) * (s_hlen + 1UL));
s_q_bef = GT_UNDEF_ULONG;
for (i = s_offset; i > 0; /**/)
{
i--;
if (q[i] != GT_UNDEF_CHAR)
{
s_q_bef = GT_HPOL_PROCESSOR_QUAL(q[i]);
break;
}
}
gt_assert(s_q_bef != GT_UNDEF_ULONG);
s_q_min = ULONG_MAX;
s_q_max = 0;
s_q_first = GT_UNDEF_ULONG;
if (!gt_aligned_segment_is_reverse(as))
{
for (i = s_offset, pos = 0; pos < s_hlen; i++)
{
if (q[i] != GT_UNDEF_CHAR)
{
s_qual[pos] = q[i];
pos++;
s_q_value = GT_HPOL_PROCESSOR_QUAL(q[i]);
if (s_q_value < s_q_min)
s_q_min = s_q_value;
if (s_q_value > s_q_max)
s_q_max = s_q_value;
if (s_q_first == GT_UNDEF_ULONG)
s_q_first = s_q_value;
s_q_last = s_q_value;
}
}
}
else
{
for (i = s_offset, pos = s_hlen; pos > 0; i++)
{
if (q[i] != GT_UNDEF_CHAR)
{
s_qual[pos - 1UL] = q[i];
pos--;
s_q_value = GT_HPOL_PROCESSOR_QUAL(q[i]);
if (s_q_value < s_q_min)
s_q_min = s_q_value;
if (s_q_value > s_q_max)
s_q_max = s_q_value;
if (s_q_first == GT_UNDEF_ULONG)
s_q_first = s_q_value;
s_q_last = s_q_value;
}
}
}
s_qual[s_hlen] = '\0';
s_q_aft = GT_UNDEF_ULONG;
for (/**/; i < gt_aligned_segment_length(as); i++)
{
if (q[i] != GT_UNDEF_CHAR)
{
s_q_aft = GT_HPOL_PROCESSOR_QUAL(q[i]);
break;
}
}
gt_assert(s_q_aft != GT_UNDEF_ULONG);
gt_assert(s_q_min < ULONG_MAX);
gt_assert(s_q_max >= s_q_min);
s_q_range = s_q_max - s_q_min + 1UL;
/* convert to 1-based coordinates */
r_hpos++;
s_hpos++;
/* handle reverse alignments */
if (gt_aligned_segment_is_reverse(as))
{
/* complement char */
GtError *err = gt_error_new();
(void)gt_complement(&s_char, s_char, err);
gt_error_delete(err);
/* correct coords on s */
s_hend = s_hpos;
s_hpos = s_hpos - s_hlen + 1UL;
s_or = '-';
/* swap q values */
s_q_value = s_q_aft;
s_q_aft = s_q_bef;
s_q_bef = s_q_value;
s_q_value = s_q_last;
s_q_last = s_q_first;
s_q_first = s_q_value;
}
else
{
s_hend = s_hpos + s_hlen - 1UL;
s_or = '+';
}
gt_file_xprintf(outfp,
"%lu\t%c\t%lu\t%lu\t%c\t%c\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu\t"
"%lu\t%lu\t%lu\t%.2f\t%lu\t%lu\t%lu\t%lu\t%s\t%s\n",
r_hpos, edit, s_hpos, s_hend, s_char, s_or, c_len, coverage, r_hlen,
r_supp, s_hlen, a_hlen, a_supp, s_mapq, s_q_bef, s_q_first, s_q_min,
s_q_ave, s_q_max, s_q_range, s_q_last, s_q_aft, s_qual, s_id);
gt_free(s_qual);
}
