int gt_extractkeysfromfastaindex(const char *indexname,
const GtStr *fileofkeystoextract,
unsigned long linewidth,GtError *err)
{
GtEncseq *encseq = NULL;
GtEncseqLoader *el = NULL;
bool haserr = false;
unsigned long numofdbsequences = 0, keysize = 0;
el = gt_encseq_loader_new();
encseq = gt_encseq_loader_load(el, indexname, err);
gt_encseq_loader_delete(el);
if (encseq == NULL)
{
haserr = true;
}
if (!haserr)
{
int retval;
numofdbsequences = gt_encseq_num_of_sequences(encseq);
retval = readkeysize(indexname,err);
if (retval < 0)
{
haserr = true;
}
keysize = (unsigned long) retval;
}
if (!haserr)
{
char *keytab;
unsigned long keytablength;
keytablength = 1UL + numofdbsequences * (keysize+1);
keytab = gt_fa_mmap_check_size_with_suffix(indexname,
GT_KEYSTABFILESUFFIX,
keytablength,
sizeof (GtUchar),
err);
if (keytab == NULL)
{
haserr = true;
} else
{
if (itersearchoverallkeys(encseq,keytab,numofdbsequences,
keysize,fileofkeystoextract,
linewidth,err) != 0)
{
haserr = true;
}
}
gt_fa_xmunmap(keytab);
}
if (encseq != NULL)
{
gt_encseq_delete(encseq);
encseq = NULL;
}
return haserr ? -1 : 0;
}
static int inputsuffixarray(bool map,
Suffixarray *suffixarray,
unsigned int demand,
const char *indexname,
GtLogger *logger,
GtError *err)
{
bool haserr = false;
GtEncseqLoader *el;
GtUword totallength = 0;
gt_error_check(err);
initsuffixarray(suffixarray);
el = gt_encseq_loader_new();
if (!(demand & SARR_DESTAB))
gt_encseq_loader_do_not_require_des_tab(el);
else
gt_encseq_loader_require_des_tab(el);
if (!(demand & SARR_SDSTAB))
gt_encseq_loader_do_not_require_sds_tab(el);
else
gt_encseq_loader_require_sds_tab(el);
if (!(demand & SARR_SSPTAB))
gt_encseq_loader_do_not_require_ssp_tab(el);
else
gt_encseq_loader_require_ssp_tab(el);
gt_encseq_loader_set_logger(el, logger);
suffixarray->encseq = gt_encseq_loader_load(el, indexname, err);
gt_encseq_loader_delete(el);
if (suffixarray->encseq == NULL)
{
haserr = true;
}
if (!haserr)
{
haserr = scanprjfileuintkeys(suffixarray,indexname,logger,err);
}
if (!haserr
&& suffixarray->mirroredencseq
&& !gt_encseq_is_mirrored(suffixarray->encseq))
{
if (gt_encseq_mirror(suffixarray->encseq, err) != 0)
haserr = true;
}
if (!haserr)
{
totallength = gt_encseq_total_length(suffixarray->encseq);
}
if (!haserr && (demand & SARR_SUFTAB))
{
if (map)
{
if (suffixarray->numberofallsortedsuffixes > 0)
{
suffixarray->suftab
= gt_fa_mmap_check_size_with_suffix(indexname,
GT_SUFTABSUFFIX,
suffixarray->numberofallsortedsuffixes,
sizeof (*suffixarray->suftab),
err);
if (suffixarray->suftab == NULL)
{
haserr = true;
}
}
} else
{
#if defined (_LP64) || defined (_WIN64)
off_t filesize = gt_file_size_with_suffix(indexname,GT_SUFTABSUFFIX);
if (filesize == (off_t) sizeof (uint32_t) *
suffixarray->numberofallsortedsuffixes)
{
gt_logger_log(logger,"read suftab in units of 4 bytes");
INITBufferedfile(indexname,&suffixarray->suftabstream_uint32_t,uint32_t,
GT_SUFTABSUFFIX);
} else
{
gt_logger_log(logger,"read suftab in units of 8 bytes");
INITBufferedfile(indexname,&suffixarray->suftabstream_GtUword,GtUword,
GT_SUFTABSUFFIX);
}
#else
gt_logger_log(logger,"read suftab in units of 4 bytes");
INITBufferedfile(indexname,&suffixarray->suftabstream_GtUword,GtUword,
GT_SUFTABSUFFIX);
#endif
}
if (!haserr && !suffixarray->longest.defined)
{
gt_error_set(err,"longest not defined");
haserr = true;
}
}
if (!haserr && (demand & SARR_LCPTAB))
{
if (map)
{
if (suffixarray->numberofallsortedsuffixes > 0)
{
suffixarray->lcptab
= gt_fa_mmap_check_size_with_suffix(indexname,
GT_LCPTABSUFFIX,
suffixarray->numberofallsortedsuffixes,
sizeof (*suffixarray->lcptab),
err);
if (suffixarray->lcptab == NULL)
{
haserr = true;
}
}
} else
{
INITBufferedfile(indexname,&suffixarray->lcptabstream,GtUchar,
GT_LCPTABSUFFIX);
if (!haserr &&
fseek(suffixarray->lcptabstream.fp,
(GtWord) sizeof (GtUchar),SEEK_SET))
{
gt_error_set(err,"fseek(esastream) failed: %s",strerror(errno));
haserr = true;
}
}
if (!haserr && !suffixarray->numoflargelcpvalues.defined)
{
gt_error_set(err,"numoflargelcpvalues not defined");
haserr = true;
}
if (!haserr && suffixarray->numoflargelcpvalues.valueunsignedlong > 0)
{
if (map)
{
suffixarray->llvtab
= gt_fa_mmap_check_size_with_suffix(indexname,
GT_LARGELCPTABSUFFIX,
(GtUword)
suffixarray->numoflargelcpvalues.
valueunsignedlong,
sizeof (*suffixarray->llvtab),
err);
if (suffixarray->llvtab == NULL)
{
haserr = true;
}
} else
{
INITBufferedfile(indexname,&suffixarray->llvtabstream,Largelcpvalue,
GT_LARGELCPTABSUFFIX);
}
}
}
if (!haserr && (demand & SARR_BWTTAB))
{
if (map)
{
suffixarray->bwttab
= gt_fa_mmap_check_size_with_suffix(indexname,
GT_BWTTABSUFFIX,
totallength+1,
sizeof (*suffixarray->bwttab),
err);
if (suffixarray->bwttab == NULL)
{
haserr = true;
}
} else
{
INITBufferedfile(indexname,&suffixarray->bwttabstream,GtUchar,
GT_BWTTABSUFFIX);
}
}
if (!haserr && (demand & SARR_BCKTAB))
{
suffixarray->bcktab
= gt_bcktab_map(indexname,
gt_encseq_alphabetnumofchars(suffixarray->encseq),
suffixarray->prefixlength,
totallength+1,
true,
err);
if (suffixarray->bcktab == NULL)
{
haserr = true;
}
}
if (haserr)
{
gt_freesuffixarray(suffixarray);
}
return haserr ? -1 : 0;
}
