void gt_Outlcpinfo_check_lcpvalues(const GtEncseq *encseq,
GtReadmode readmode,
const GtSuffixsortspace *sortedsample,
GtUword effectivesamplesize,
const GtOutlcpinfo *outlcpinfosample,
bool checkequality)
{
GT_UNUSED int cmp;
GtUword idx, reallcp, startpos1, startpos2, currentlcp,
totalcmpmissing = 0;
if (effectivesamplesize == 0)
{
return;
}
startpos1 = gt_suffixsortspace_getdirect(sortedsample,0);
for (idx=1UL; idx<effectivesamplesize; idx++)
{
startpos2 = gt_suffixsortspace_getdirect(sortedsample,idx);
cmp = gt_encseq_check_comparetwosuffixes(encseq,
readmode,
&reallcp,
false,
false,
0,
startpos1,
startpos2,
NULL,
NULL);
gt_assert(cmp <= 0);
gt_assert(GT_ISIBITSET(outlcpinfosample->lcpsubtab.tableoflcpvalues
.isset,idx));
currentlcp = (GtUword) outlcpinfosample->lcpsubtab.tableoflcpvalues.
bucketoflcpvalues[idx];
if ((checkequality && currentlcp != reallcp) ||
(!checkequality && currentlcp > reallcp))
{
fprintf(stderr,"idx="GT_WU",suffixpair="GT_WU","GT_WU": "
"currentlcp = "GT_WU" %s "GT_WU" = reallcp\n",
idx,startpos1,startpos2,currentlcp,
checkequality ? "!=" : ">",reallcp);
gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,startpos1,50UL);
fprintf(stderr,"\n");
gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,startpos2,50UL);
fprintf(stderr,"\n");
exit(GT_EXIT_PROGRAMMING_ERROR);
} else
{
totalcmpmissing += (reallcp - currentlcp);
}
startpos1 = startpos2;
}
/*printf("totalcmpmissing = "GT_WU"(avg=%.2f)\n",
totalcmpmissing,(double) totalcmpmissing/effectivesamplesize);*/
}
static void backwardderive(const GtBucketspec2 *bucketspec2,
GtSuffixsortspace *suffixsortspace,
GtUword *targetoffset,
unsigned int source,
GtUword idx)
{
GtUword startpos;
GtUchar cc;
for (; idx + 1 > targetoffset[source] + 1; idx--)
{
startpos = gt_suffixsortspace_getdirect(suffixsortspace,idx);
if (startpos > 0)
{
cc = gt_encseq_get_encoded_char(bucketspec2->encseq,
startpos-1,
bucketspec2->readmode);
if (ISNOTSPECIAL(cc) && !bucketspec2->superbuckettab[cc].sorted)
{
gt_suffixsortspace_setdirect(suffixsortspace,targetoffset[cc],
startpos - 1);
targetoffset[cc]--;
}
}
}
}
unsigned long gt_suffixsortspace_get(const GtSuffixsortspace *sssp,
unsigned long subbucketleft,
unsigned long idx)
{
return gt_suffixsortspace_getdirect(sssp, sssp->bucketleftidx
+ subbucketleft
+ idx
- sssp->partoffset);
}
GtUword gt_suffixsortspace_get(const GtSuffixsortspace *sssp,
GtUword subbucketleft,
GtUword idx)
{
return gt_suffixsortspace_getdirect(sssp, sssp->bucketleftidx
+ subbucketleft
+ idx
- sssp->partoffset);
}
void gt_suffixsortspace_checkorder(const GtSuffixsortspace *sssp,
unsigned long subbucketleft,
unsigned long width)
{
unsigned long idx, currentpos;
GT_UNUSED unsigned long prevpos;
gt_assert(width > 0);
prevpos = gt_suffixsortspace_getdirect(sssp,
sssp->bucketleftidx+subbucketleft -
sssp->partoffset);
for (idx=sssp->bucketleftidx+subbucketleft - sssp->partoffset + 1;
idx<sssp->bucketleftidx+subbucketleft + width - sssp->partoffset;
idx++)
{
currentpos = gt_suffixsortspace_getdirect(sssp,idx);
gt_assert(prevpos > currentpos);
prevpos = currentpos;
}
}
void gt_suffixsortspace_showrange(const GtSuffixsortspace *sssp,
unsigned long subbucketleft,
unsigned long width)
{
unsigned long idx;
printf("%lu,%lu=",sssp->bucketleftidx+subbucketleft-sssp->partoffset,
sssp->bucketleftidx+subbucketleft+width-1-sssp->partoffset);
for (idx=sssp->bucketleftidx+subbucketleft-sssp->partoffset;
idx<sssp->bucketleftidx+subbucketleft+width-sssp->partoffset;
idx++)
{
printf(" %lu", gt_suffixsortspace_getdirect(sssp,idx));
}
}
void gt_suffixsortspace_showrange(const GtSuffixsortspace *sssp,
GtUword subbucketleft,
GtUword width)
{
GtUword idx;
printf(""GT_WU","GT_WU"=",sssp->bucketleftidx+subbucketleft-sssp->partoffset,
sssp->bucketleftidx+subbucketleft+width-1-sssp->partoffset);
for (idx=sssp->bucketleftidx+subbucketleft-sssp->partoffset;
idx<sssp->bucketleftidx+subbucketleft+width-sssp->partoffset;
idx++)
{
printf(" "GT_WU"", gt_suffixsortspace_getdirect(sssp,idx));
}
}
size_t gt_translateSuftab2BWTSuffixsortspace(
void *translator,
void *voiddest,
const GtSuffixsortspace *suffixsortspace,
unsigned long offset,
size_t len)
{
struct encSeqTrState *trState = (struct encSeqTrState *) translator;
GtUchar *dest = (GtUchar *) voiddest;
size_t idx;
gt_assert(trState);
for (idx = 0; idx < len; ++idx)
{
dest[idx]
= sfxIdx2BWTSym(gt_suffixsortspace_getdirect(suffixsortspace,offset+idx),
trState->encseq, trState->readmode);
}
return len * sizeof (GtUchar);
}
static int gt_seqorder_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, void *tool_arguments, GtError *err)
{
GtSeqorderArguments *arguments = tool_arguments;
int had_err = 0;
GtEncseq *encseq;
GtEncseqLoader *loader;
unsigned long i, nofseqs;
gt_error_check(err);
gt_assert(arguments != NULL);
/* load encseq */
loader = gt_encseq_loader_new();
encseq = gt_encseq_loader_load(loader, argv[parsed_args], err);
if (encseq == NULL)
had_err = -1;
if (had_err == 0 && !gt_encseq_has_description_support(encseq))
gt_warning("%s has no description support", argv[parsed_args]);
if (!had_err)
{
nofseqs = gt_encseq_num_of_sequences(encseq);
if (arguments->invert)
{
for (i = nofseqs; i > 0; i--)
gt_seqorder_output(i - 1, encseq);
}
else if (arguments->shuffle)
{
unsigned long *seqnums;
seqnums = gt_malloc(sizeof (unsigned long) * nofseqs);
gt_seqorder_get_shuffled_seqnums(nofseqs, seqnums);
for (i = 0; i < nofseqs; i++)
gt_seqorder_output(seqnums[i], encseq);
gt_free(seqnums);
}
else
{
GtSuffixsortspace *suffixsortspace;
gt_assert(arguments->sort || arguments->revsort);
suffixsortspace
= gt_suffixsortspace_new(nofseqs,
/* Use iterator over sequence separators:
saves a lot of binary searches */
gt_encseq_seqstartpos(encseq, nofseqs-1),
false,NULL);
gt_seqorder_sort(suffixsortspace, encseq);
if (arguments->sort)
for (i = 0; i < nofseqs; i++)
gt_seqorder_output(gt_encseq_seqnum(encseq,
gt_suffixsortspace_getdirect(suffixsortspace, i)), encseq);
else
for (i = nofseqs; i > 0; i--)
gt_seqorder_output(gt_encseq_seqnum(encseq,
gt_suffixsortspace_getdirect(suffixsortspace, i - 1)), encseq);
gt_suffixsortspace_delete(suffixsortspace, false);
}
}
gt_encseq_loader_delete(loader);
gt_encseq_delete(encseq);
return had_err;
}
void gt_copysort_derivesorting(const GtBucketspec2 *bucketspec2,
GtSuffixsortspace *suffixsortspace,
GtLogger *logger)
{
GtUword hardwork = 0,
*targetoffset;
unsigned int idx, idxsource, source, second;
#ifdef WITHSUFFIXES
{
GtUword idx;
for (idx = 0; idx < bucketspec2->partwidth; idx++)
{
gt_encseq_showatstartpos(
stdout,
GT_ISDIRREVERSE(readmode) ? false : true,
GT_ISDIRCOMPLEMENT(readmode) ? true : false,
encseq,
gt_suffixsortspace_getdirect(suffixsortspace,idx));
}
}
#endif
targetoffset = gt_malloc(sizeof (*targetoffset) * bucketspec2->numofchars);
for (idxsource = 0; idxsource<bucketspec2->numofchars; idxsource++)
{
source = bucketspec2->order[idxsource];
for (second = 0; second < bucketspec2->numofchars; second++)
{
if (!bucketspec2->subbuckettab[source][second].sorted && source != second)
{
gt_assert(bucketspec2->subbuckettab[source][second].hardworktodo);
gt_logger_log(logger,"hard work for %u %u",source,second);
hardwork += getendidx(bucketspec2,source,second) -
getstartidx(bucketspec2,source,second);
bucketspec2->subbuckettab[source][second].sorted = true;
} else
{
gt_assert(!bucketspec2->subbuckettab[source][second].hardworktodo);
}
}
if (getstartidx(bucketspec2,source,0) <
getstartidx(bucketspec2,source,source))
{
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
targetoffset[idx] = getstartidx(bucketspec2,idx,source);
}
forwardderive(bucketspec2,
suffixsortspace,
targetoffset,
source,
getstartidx(bucketspec2,source,0));
}
if (getendidx(bucketspec2,source,source) <
getendidx(bucketspec2,source,bucketspec2->numofchars))
{
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
/* do not need to assert that getendidx(idx,source) > 0, as later the
value stored in targetoffset is incremented */
targetoffset[idx] = getendidx(bucketspec2,idx,source) - 1;
}
gt_assert(getendidx(bucketspec2,source,bucketspec2->numofchars) > 0);
backwardderive(bucketspec2,
suffixsortspace,
targetoffset,
source,
getendidx(bucketspec2,source,bucketspec2->numofchars) - 1);
}
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
bucketspec2->subbuckettab[idx][source].sorted = true;
}
bucketspec2->superbuckettab[source].sorted = true;
}
gt_free(targetoffset);
gt_logger_log(logger,"hardwork = "GT_WU" (%.2f)",
hardwork,
(double) hardwork/gt_encseq_total_length(bucketspec2->encseq));
}