static bool chain_is_filled_and_consistent(GthChain *chain,
unsigned long gen_total_length,
unsigned long gen_offset)
{
GtArray *testranges;
/* check of file sequence numbers are defined */
if (chain->gen_file_num == GT_UNDEF_ULONG ||
chain->gen_seq_num == GT_UNDEF_ULONG ||
chain->ref_file_num == GT_UNDEF_ULONG ||
chain->ref_seq_num == GT_UNDEF_ULONG) {
return false;
}
if (!gt_ranges_are_consecutive(chain->forwardranges))
return false;
testranges = gt_array_new(sizeof (GtRange));
gt_ranges_copy_to_opposite_strand(testranges, chain->reverseranges,
gen_total_length, gen_offset);
if (!gt_ranges_are_equal(testranges, chain->forwardranges)) {
gt_array_delete(testranges);
return false;
}
gt_array_delete(testranges);
return true;
}
bool gth_sa_exons_are_forward_and_consecutive(const GthSA *sa)
{
GtArray *ranges;
gt_assert(sa);
ranges = gt_array_new(sizeof (GtRange));
gth_sa_get_exons(sa, ranges);
if (!gt_ranges_are_consecutive(ranges)) {
gt_array_delete(ranges);
return false;
}
gt_array_delete(ranges);
return true;
}
void gth_save_chain(GtChain *chain, GtFragment *fragments,
unsigned long num_of_fragments,
GT_UNUSED unsigned long max_gap_width,
void *data)
{
GthSaveChainInfo *info = (GthSaveChainInfo*) data;
GtRange range;
GthChain *gth_chain;
unsigned long i, fragnum;
gt_assert(chain_is_colinear(chain, fragments));
if (info->comments) {
gt_file_xprintf(info->outfp, "%c process global chain with score %ld\n",
COMMENTCHAR, gt_chain_get_score(chain));
gt_file_xprintf(info->outfp, "%c process global chain with the "
"following fragments\n", COMMENTCHAR);
for (i = 0; i < gt_chain_size(chain); i++)
showfragment(fragments + gt_chain_get_fragnum(chain, i), info->outfp);
}
/* init */
gth_chain = gth_chain_new();
gth_chain->gen_file_num = info->gen_file_num;
gth_chain->gen_seq_num = info->gen_seq_num;
gth_chain->ref_file_num = info->ref_file_num;
gth_chain->ref_seq_num = info->ref_seq_num;
/* chain has a minimum length of 1 */
gt_assert(gt_chain_size(chain));
/* global chain filter */
if (globalchainislongenough(chain, fragments,
>h_chain->refseqcoverage, info->gcmincoverage,
info->referencelength, info->stat, info->comments,
info->outfp)) {
/* save all potential exons */
for (i = 0; i < gt_chain_size(chain); i++) {
fragnum = gt_chain_get_fragnum(chain, i);
range.start = fragments[fragnum].startpos2;
range.end = fragments[fragnum].endpos2;
/* check for overlap */
if (i > 0 &&
range.start <=
((GtRange*) gt_array_get_last(gth_chain->forwardranges))->end) {
/* overlap found -> modify last range */
gt_assert(((GtRange*) gt_array_get_last(gth_chain->forwardranges))
->end <= range.end);
((GtRange*) gt_array_get_last(gth_chain->forwardranges))->end =
range.end;
}
else {
#ifndef NDEBUG
if (i > 0) {
/* gap width is smaller or equal than the maximum gap width */
gt_assert((range.start - 1 -
((GtRange*) gt_array_get_last(gth_chain->forwardranges))
->end + 1 - 1) <= max_gap_width);
}
#endif
/* save range */
gt_array_add(gth_chain->forwardranges, range);
}
}
GtRange genomicrange = chain_get_genomicrange(gth_chain);
if (info->enrichchains) {
enrich_chain(gth_chain, fragments, num_of_fragments, info->comments,
info->outfp);
}
gt_assert(gt_ranges_are_consecutive(gth_chain->forwardranges));
/* copy ranges to opposite strand */
gt_ranges_copy_to_opposite_strand(gth_chain->reverseranges,
gth_chain->forwardranges,
info->gen_total_length,
info->gen_offset);
/* compute jump table if necessary */
if (info->jump_table) {
GthJumpTable *forward_jump_table, *reverse_jump_table;
GtArray *chain_fragments;
chain_fragments = make_list_of_chain_fragments(chain, fragments,
num_of_fragments,
info->enrichchains,
&genomicrange);
forward_jump_table =
info->jump_table_new(gt_array_get_space(chain_fragments),
gt_array_size(chain_fragments), info->jtdebug);
reverse_jump_table =
info->jump_table_new_reverse(forward_jump_table,
info->gen_total_length, info->gen_offset,
info->ref_total_length, info->ref_offset);
gt_assert(!gth_chain->forward_jump_table);
gth_chain->forward_jump_table = forward_jump_table;
gt_assert(!gth_chain->reverse_jump_table);
gth_chain->reverse_jump_table = reverse_jump_table;
gt_array_delete(chain_fragments);
gth_chain->jump_table_delete = info->jump_table_delete;
}
/* save array of potential exons */
gth_chain_collection_add(info->chain_collection, gth_chain);
if (info->comments) {
gt_file_xprintf(info->outfp, "%c global chain with the following "
"ranges has been saved\n",COMMENTCHAR);
gt_file_xprintf(info->outfp, "%c forward ranges:\n", COMMENTCHAR);
gt_file_xprintf(info->outfp, "%c ", COMMENTCHAR);
gt_ranges_show(gth_chain->forwardranges, info->outfp);
gt_file_xprintf(info->outfp, "%c reverse ranges:\n", COMMENTCHAR);
gt_file_xprintf(info->outfp, "%c ", COMMENTCHAR);
gt_ranges_show(gth_chain->reverseranges, info->outfp);
}
/* output stored chains here
(Mohamed needed this to compare the chaining phase of gth with CHAINER)
*/
if (info->stopafterchaining) {
gt_file_xprintf(info->outfp,
"%c gl. chain with coverage=%.2f and score %ld "
"(genseq=%lu, str.=%c, refseq=%lu)\n", COMMENTCHAR,
gth_chain->refseqcoverage, gt_chain_get_score(chain),
gth_chain->gen_seq_num, SHOWSTRAND(info->directmatches),
gth_chain->ref_seq_num);
for (i = 0; i < gt_chain_size(chain); i++)
showfragment(fragments + gt_chain_get_fragnum(chain, i), info->outfp);
}
}
else {
/* for -paralogs this case is not supposed to occur */
gt_assert(!info->paralogs);
if (info->comments)
gt_file_xprintf(info->outfp, "%c global chain discarded\n",
COMMENTCHAR);
gth_chain_delete(gth_chain);
}
}
/* XXX: change this function: add more sophisticated extension strategy */
void gth_chain_extend_borders(GthChain *chain, const GtRange *gen_seq_bounds,
const GtRange *gen_seq_bounds_rc,
GT_UNUSED unsigned long gen_total_length,
GT_UNUSED unsigned long gen_offset)
{
long tmpborder;
/* at least one range in chain */
gt_assert(gt_array_size(chain->forwardranges));
/* forward range borders are in considered genomic region */
gt_assert(gt_ranges_borders_are_in_region(chain->forwardranges,
gen_seq_bounds));
/* reverse range borders are in considered genomic region */
gt_assert(gt_ranges_borders_are_in_region(chain->reverseranges,
gen_seq_bounds_rc));
/* chain->forwardranges is forward and consecutive */
gt_assert(gt_ranges_are_consecutive(chain->forwardranges));
/* valid sequence bounds */
gt_assert(gen_seq_bounds->start <= gen_seq_bounds->end);
gt_assert(gen_seq_bounds_rc->start <= gen_seq_bounds_rc->end);
/* set start border, forward strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_first(chain->forwardranges))
->start);
tmpborder -= DPEXTENSION;
if (tmpborder < gt_safe_cast2long(gen_seq_bounds->start))
tmpborder = gen_seq_bounds->start;
((GtRange*) gt_array_get_first(chain->forwardranges))->start =
gt_safe_cast2ulong(tmpborder);
/* set start border, reverse complement strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_first(chain->reverseranges))
->start);
tmpborder -= DPEXTENSION;
if (tmpborder < gt_safe_cast2long(gen_seq_bounds_rc->start))
tmpborder = gen_seq_bounds_rc->start;
((GtRange*) gt_array_get_first(chain->reverseranges))->start =
gt_safe_cast2ulong(tmpborder);
/* set end border, forward strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_last(chain->forwardranges))
->end);
tmpborder += DPEXTENSION;
if (tmpborder > gt_safe_cast2long(gen_seq_bounds->end))
tmpborder = gen_seq_bounds->end;
((GtRange*) gt_array_get_last(chain->forwardranges))->end =
gt_safe_cast2ulong(tmpborder);
/* set end border, reverse complement strand */
tmpborder = gt_safe_cast2long(((GtRange*)
gt_array_get_last(chain->reverseranges))
->end);
tmpborder += DPEXTENSION;
if (tmpborder > gt_safe_cast2long(gen_seq_bounds_rc->end))
tmpborder = gen_seq_bounds_rc->end;
((GtRange*) gt_array_get_last(chain->reverseranges))->end =
gt_safe_cast2ulong(tmpborder);
gt_assert(chain_is_filled_and_consistent(chain, gen_total_length,
gen_offset));
}
