/**
* @param alphabet ownership of alphabet is with the newly produced
* sequence object if return value is not 0
*/
static int
initBWTSeqFromEncSeqIdx(BWTSeq *bwtSeq, struct encIdxSeq *seqIdx,
MRAEnc *alphabet, GtUword *counts,
enum rangeSortMode *rangeSort,
const enum rangeSortMode *defaultRangeSort)
{
size_t alphabetSize;
Symbol bwtTerminatorFlat;
EISHint hint;
gt_assert(bwtSeq && seqIdx);
bwtSeq->alphabet = alphabet;
alphabetSize = gt_MRAEncGetSize(alphabet);
if (!alphabetSize)
/* weird error, shouldn't happen, but I prefer error return to
* segfault in case someone tampered with the input */
return 0;
/* FIXME: this should probably be handled in chardef.h to have a
* unique mapping */
/* FIXME: this assumes there is exactly two ranges */
gt_MRAEncAddSymbolToRange(alphabet, bwtTerminatorSym, 1);
gt_assert(gt_MRAEncGetSize(alphabet) == alphabetSize + 1);
alphabetSize = gt_MRAEncGetSize(alphabet);
bwtSeq->bwtTerminatorFallback = bwtTerminatorFlat
= MRAEncMapSymbol(alphabet, UNDEFBWTCHAR);
bwtSeq->bwtTerminatorFallbackRange = 1;
bwtSeq->count = counts;
bwtSeq->rangeSort = rangeSort;
bwtSeq->seqIdx = seqIdx;
bwtSeq->alphabetSize = alphabetSize;
bwtSeq->hint = hint = newEISHint(seqIdx);
{
Symbol i;
GtUword len = EISLength(seqIdx), *count = bwtSeq->count;
count[0] = 0;
for (i = 0; i < bwtTerminatorFlat; ++i)
count[i + 1] = count[i]
+ EISSymTransformedRank(seqIdx, i, len, hint);
/* handle character which the terminator has been mapped to specially */
count[i + 1] = count[i]
+ EISSymTransformedRank(seqIdx, i, len, hint) - 1;
gt_assert(count[i + 1] >= count[i]);
/* now we can finish the rest of the symbols */
for (i += 2; i < alphabetSize; ++i)
count[i] = count[i - 1]
+ EISSymTransformedRank(seqIdx, i - 1, len, hint);
/* and finally place the 1-count for the terminator */
count[i] = count[i - 1] + 1;
#ifdef EIS_DEBUG
gt_log_log("count[alphabetSize]="GT_WU", len="GT_WU"",count[alphabetSize],
len);
for (i = 0; i <= alphabetSize; ++i)
gt_log_log("count[%u]="GT_WU"", (unsigned)i, count[i]);
#endif
gt_assert(count[alphabetSize] == len);
}
gt_BWTSeqInitLocateHandling(bwtSeq, defaultRangeSort);
return 1;
}
extern int
gt_packedindex_chk_integrity(int argc, const char *argv[], GtError *err)
{
struct encIdxSeq *seq;
struct chkIndexOptions params;
GtStr *inputProject;
int parsedArgs;
int had_err = 0;
Verboseinfo *verbosity = NULL;
gt_error_check(err);
switch (parseChkIndexOptions(&parsedArgs, argc, argv, ¶ms, err))
{
case OPTIONPARSER_OK:
break;
case OPTIONPARSER_ERROR:
return -1;
case OPTIONPARSER_REQUESTS_EXIT:
return 0;
}
inputProject = gt_str_new_cstr(argv[parsedArgs]);
verbosity = newverboseinfo(params.verboseOutput);
seq = loadEncIdxSeq(inputProject, params.encType, params.EISFeatureSet,
verbosity, err);
if ((had_err = seq == NULL))
{
gt_error_set(err, "Failed to load index: %s", gt_str_get(inputProject));
}
else
{
fprintf(stderr, "# Using index over sequence "FormatSeqpos
" symbols long.\n", EISLength(seq));
{
int corrupt
= EISVerifyIntegrity(seq, inputProject, params.skipCount,
params.progressInterval, stderr,
params.checkFlags, verbosity, err);
if ((had_err = corrupt != 0))
{
fputs(gt_error_get(err), stderr); fputs("\n", stderr);
gt_error_set(err, "Integrity check failed for index: %s",
EISIntegrityCheckResultStrings[corrupt]);
}
}
}
if (seq) deleteEncIdxSeq(seq);
if (inputProject) gt_str_delete(inputProject);
if (verbosity) freeverboseinfo(&verbosity);
return had_err?-1:0;
}
