GtRange gth_seq_con_get_relative_range(GthSeqCon *seq_con,
unsigned long seq_num)
{
GtRange relative_range, range;
gt_assert(seq_con);
gt_assert(seq_num < gth_seq_con_num_of_seqs(seq_con));
range = gth_seq_con_get_range(seq_con, seq_num);
relative_range.start = 0;
relative_range.end = range.end - range.start;
return relative_range;
}
static void calc_chains_from_matches(GthChainCollection *chain_collection,
GtArray *matches,
GthChainingInfo *chaining_info,
GthSeqCon *gen_seq_con,
GthSeqCon *ref_seq_con,
GtUword rare,
double fragweightfactor,
GthJumpTableNew jump_table_new,
GthJumpTableNewReverse
jump_table_new_reverse,
GthJumpTableDelete jump_table_delete)
{
GtUword i, numofchains = 0, num_of_fragments, maxbucketlength = 0;
GtRange range;
GtFile *outfp = chaining_info->call_info->out->outfp;
GtFragment *fragments;
GthSaveChainInfo info;
GtArray *buckets;
Bucket *bucket;
/* this is a random sample to check that no equal matches exist
either one match to chain or if more than one the first two differ */
gt_assert(gt_array_size(matches) == 1 ||
(gt_array_size(matches) > 1 &&
!gth_matches_are_equal(gt_array_get(matches, 0),
gt_array_get(matches, 1))));
/* init */
buckets = gt_array_new(sizeof (Bucket));
/* output unsorted matches */
if (chaining_info->call_info->out->comments) {
gt_file_xprintf(outfp, "%c output unsorted matches\n", COMMENTCHAR);
showmatches(gt_array_get_space(matches), gt_array_size(matches), outfp);
}
/* transform reference sequence positions to opposite strand if necessary */
if (!chaining_info->directmatches) {
if (chaining_info->call_info->out->comments) {
gt_file_xprintf(outfp, "%c\n", COMMENTCHAR);
gt_file_xprintf(outfp, "%c transform reference sequence positions to "
"opposite strand\n", COMMENTCHAR);
gt_file_xprintf(outfp, "%c\n", COMMENTCHAR);
}
transform_refseq_positions(matches, ref_seq_con);
/* output transformed matches */
if (chaining_info->call_info->out->comments) {
gt_file_xprintf(outfp, "%c output transformed matches\n", COMMENTCHAR);
showmatches(gt_array_get_space(matches), gt_array_size(matches), outfp);
}
}
/* sort matches */
sort_matches_and_calc_buckets(matches, buckets, &maxbucketlength);
/* output sorted matches */
if (chaining_info->call_info->out->comments) {
gt_file_xprintf(outfp, "%c output sorted matches\n", COMMENTCHAR);
showmatches(gt_array_get_space(matches), gt_array_size(matches), outfp);
}
/* output buckets */
if (chaining_info->call_info->out->comments) {
gt_file_xprintf(outfp, "%c output buckets\n", COMMENTCHAR);
outputbuckets(buckets, gt_array_get_space(matches), outfp);
}
/* alloc space for fragments */
fragments = gt_malloc(sizeof (GtFragment) * maxbucketlength);
/* save data to process the chains with saveChainasDPrange; constant part */
info.chain_collection = chain_collection;
info.gcmincoverage = chaining_info->call_info->gcmincoverage;
info.stat = chaining_info->stat;
info.comments = chaining_info->call_info->out->comments;
info.stopafterchaining = chaining_info->call_info->simfilterparam
.stopafterchaining;
info.paralogs = chaining_info->call_info->simfilterparam.paralogs;
info.enrichchains = chaining_info->call_info->simfilterparam
.enrichchains;
info.jump_table = chaining_info->call_info->simfilterparam.jump_table;
info.jump_table_new = jump_table_new;
info.jump_table_new_reverse = jump_table_new_reverse;
info.jump_table_delete = jump_table_delete;
info.jtdebug = chaining_info->jtdebug;
info.directmatches = chaining_info->directmatches;
info.outfp = outfp;
info.gen_file_num = chaining_info->gen_file_num;
info.ref_file_num = chaining_info->ref_file_num;
/* for every bucket a chain and for every chain a DP call (later maybe more
than one chain) */
for (i = 0; i < gt_array_size(buckets); i++) {
bucket = gt_array_get(buckets, i);
if (chaining_info->call_info->out->showverbose) {
if (chaining_info->refseqisindex &&
!chaining_info->call_info->simfilterparam.online) {
/* in this case the exact number of chains is known */
numofchains = gt_array_size(buckets);
}
else {
/* this expression gives an upper bound on the number of chains
(because we do not know the exact number here) */
numofchains = chaining_info->bucketnum +
gth_seq_con_num_of_seqs(gen_seq_con) *
(gth_seq_con_num_of_seqs(ref_seq_con) - bucket->seqnum1);
if (numofchains > chaining_info->maxbucketnum)
numofchains = chaining_info->maxbucketnum;
else
chaining_info->maxbucketnum = numofchains;
}
}
/* compute a set of fragments from every bucket of matches */
gthinitfragments(fragments, &num_of_fragments,
(GthMatch*) gt_array_get_space(matches) + bucket->startpos,
bucket->length, rare, fragweightfactor);
if (chaining_info->call_info->out->showverbose) {
show_chain_calc_status (chaining_info->call_info->out->showverbose,
++chaining_info->bucketnum, numofchains,
num_of_fragments, chaining_info->gen_file_num,
gth_input_num_of_gen_files(chaining_info->input),
chaining_info->ref_file_num,
gth_input_num_of_ref_files(chaining_info->input),
chaining_info->directmatches,
chaining_info->call_info->out->verboseseqs,
bucket->seqnum2, bucket->seqnum1);
}
info.gen_seq_num = ((GthMatch*) gt_array_get(matches, bucket->startpos))
->Storeseqnumgenomic;
info.ref_seq_num = ((GthMatch*) gt_array_get(matches, bucket->startpos))
->Storeseqnumreference;
/* store genomic offset */
range = gth_seq_con_get_range(gen_seq_con, info.gen_seq_num);
info.gen_total_length = range.end - range.start + 1;
info.gen_offset = range.start;
/* store length of reference sequence */
range = gth_seq_con_get_range(ref_seq_con, info.ref_seq_num);
info.ref_total_length = range.end - range.start + 1;
info.ref_offset = range.start;
info.referencelength = range.end - range.start + 1;
/* set number of remaining buckets */
info.numofremainingbuckets = gt_array_size(buckets) - i;
if (chaining_info->call_info->simfilterparam.paralogs) {
gt_globalchaining_coverage(fragments, num_of_fragments,
chaining_info->call_info->gcmaxgapwidth,
info.referencelength,
((double)
chaining_info->call_info->gcmincoverage) /
100.0, gth_save_chain, &info);
}
else {
gt_globalchaining_max(fragments, num_of_fragments,
chaining_info->call_info->gcmaxgapwidth,
gth_save_chain, &info);
}
}
/* free space */
gt_array_delete(buckets);
gt_free(fragments);
}
