static int encseq_lua_has_multiseq_support(lua_State *L)
{
GtEncseq **encseq;
encseq = check_encseq(L, 1);
lua_pushboolean(L, gt_encseq_has_multiseq_support(*encseq));
return 1;
}
static void gt_querysubstringmatch(bool selfmatch,
const GtEncseq *dbencseq,
const ESASuffixptr *suftabpart,
GtReadmode readmode,
GtUword numberofsuffixes,
uint64_t queryunitnum,
GtQueryrepresentation *queryrep,
GtUword minmatchlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtQuerymatch *querymatchspaceptr)
{
GtMMsearchiterator *mmsi;
GtUword totallength, localqueryoffset = 0;
uint64_t localqueryunitnum = queryunitnum;
GtQuerysubstring querysubstring;
gt_assert(numberofsuffixes > 0);
totallength = gt_encseq_total_length(dbencseq);
querysubstring.queryrep = queryrep;
for (querysubstring.currentoffset = 0;
querysubstring.currentoffset <= queryrep->seqlen - minmatchlength;
querysubstring.currentoffset++)
{
GtUword dbstart;
mmsi = gt_mmsearchiterator_new(dbencseq,
suftabpart,
0, /* leftbound */
numberofsuffixes - 1, /* rightbound */
0, /* offset */
readmode,
&querysubstring,
minmatchlength);
while (gt_mmsearchiterator_next(&dbstart,mmsi))
{
if (gt_mmsearch_isleftmaximal(dbencseq,
readmode,
dbstart,
&querysubstring))
{
GtUword dbseqnum, dbseqstartpos, dbseqlen, extend;
extend = gt_mmsearch_extendright(dbencseq,
mmsi->esr,
readmode,
totallength,
dbstart + minmatchlength,
&querysubstring,
minmatchlength);
if (gt_encseq_has_multiseq_support(dbencseq))
{
dbseqnum = gt_encseq_seqnum(dbencseq,dbstart);
dbseqstartpos = gt_encseq_seqstartpos(dbencseq,dbseqnum);
dbseqlen = gt_encseq_seqlength(dbencseq,dbseqnum);
} else
{
dbseqnum = dbseqstartpos = dbseqlen = 0;
}
gt_querymatch_init(querymatchspaceptr,
minmatchlength + extend,
dbstart,
dbseqnum,
dbstart - dbseqstartpos,
dbseqlen,
0, /* score */
0, /* edist */
selfmatch,
localqueryunitnum,
minmatchlength + extend,
localqueryoffset,
queryrep->seqlen);
processquerymatch(processquerymatchinfo,querymatchspaceptr);
}
}
gt_mmsearchiterator_delete(mmsi);
mmsi = NULL;
if (gt_mmsearch_accessquery(queryrep,querysubstring.currentoffset)
== (GtUchar) SEPARATOR)
{
localqueryunitnum++;
localqueryoffset = 0;
} else
{
localqueryoffset++;
}
}
}
static int gt_encseq_check_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, void *tool_arguments,
GtError *err)
{
GtEncseqCheckArguments *arguments = tool_arguments;
int had_err = 0;
GtEncseqLoader *encseq_loader;
GtEncseq *encseq;
gt_error_check(err);
gt_assert(arguments);
encseq_loader = gt_encseq_loader_new();
if (!(encseq = gt_encseq_loader_load(encseq_loader, argv[parsed_args], err)))
had_err = -1;
if (!had_err) {
int readmode;
gt_encseq_check_startpositions(encseq);
for (readmode = 0; readmode < 4; readmode++)
{
if (gt_alphabet_is_dna(gt_encseq_alphabet(encseq)) ||
((GtReadmode) readmode) == GT_READMODE_FORWARD ||
((GtReadmode) readmode) == GT_READMODE_REVERSE)
{
if (gt_encseq_check_consistency(encseq,
gt_encseq_filenames(encseq),
(GtReadmode) readmode,
arguments->scantrials,
arguments->multicharcmptrials,
gt_encseq_has_multiseq_support(encseq),
err) != 0)
{
had_err = -1;
break;
}
}
}
if (!had_err)
{
gt_encseq_check_specialranges(encseq);
}
if (!had_err)
{
gt_encseq_check_markpos(encseq);
}
if (!had_err)
{
had_err = gt_encseq_check_minmax(encseq, err);
}
if (!had_err &&
arguments->prefixlength > 0)
{
if (gt_verifymappedstr(encseq,
arguments->prefixlength,
err) != 0)
{
had_err = -1;
}
}
}
gt_encseq_delete(encseq);
gt_encseq_loader_delete(encseq_loader);
return had_err;
}
static int gt_encseq_info_runner(GT_UNUSED int argc, const char **argv,
int parsed_args, void *tool_arguments,
GtError *err)
{
GtEncseqInfoArguments *arguments = tool_arguments;
int had_err = 0;
GtAlphabet *alpha;
const GtUchar *chars;
gt_error_check(err);
gt_assert(arguments);
if (arguments->nomap) {
GtEncseqMetadata *emd = gt_encseq_metadata_new(argv[parsed_args], err);
if (!emd)
had_err = -1;
if (!had_err) {
if (!arguments->noindexname) {
gt_file_xprintf(arguments->outfp, "index name: ");
gt_file_xprintf(arguments->outfp, "%s\n", argv[parsed_args]);
}
gt_file_xprintf(arguments->outfp, "file format version: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_metadata_version(emd));
gt_file_xprintf(arguments->outfp, "64-bit file: ");
gt_file_xprintf(arguments->outfp, "%s\n", gt_encseq_metadata_is64bit(emd)
? "yes"
: "no");
gt_file_xprintf(arguments->outfp, "total length: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_metadata_total_length(emd));
gt_file_xprintf(arguments->outfp, "number of sequences: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_metadata_num_of_sequences(emd));
gt_file_xprintf(arguments->outfp, "number of files: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_metadata_num_of_files(emd));
gt_file_xprintf(arguments->outfp, "length of shortest/longest "
"sequence: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"/"GT_WU"\n",
gt_encseq_metadata_min_seq_length(emd),
gt_encseq_metadata_max_seq_length(emd));
gt_file_xprintf(arguments->outfp, "accesstype: ");
gt_file_xprintf(arguments->outfp, "%s\n",
gt_encseq_access_type_str(gt_encseq_metadata_accesstype(emd)));
alpha = gt_encseq_metadata_alphabet(emd);
chars = gt_alphabet_characters(alpha);
gt_file_xprintf(arguments->outfp, "alphabet size: ");
gt_file_xprintf(arguments->outfp, "%u\n",
gt_alphabet_num_of_chars(alpha));
gt_file_xprintf(arguments->outfp, "alphabet characters: ");
gt_file_xprintf(arguments->outfp, "%.*s", gt_alphabet_num_of_chars(alpha),
(char*) chars);
if (gt_alphabet_is_dna(alpha))
gt_file_xprintf(arguments->outfp, " (DNA)");
if (gt_alphabet_is_protein(alpha))
gt_file_xprintf(arguments->outfp, " (Protein)");
gt_file_xprintf(arguments->outfp, "\n");
if (arguments->show_alphabet) {
GtStr *out = gt_str_new();
gt_alphabet_to_str(alpha, out);
gt_file_xprintf(arguments->outfp, "alphabet definition:\n");
gt_file_xprintf(arguments->outfp, "%s\n", gt_str_get(out));
gt_str_delete(out);
}
}
gt_encseq_metadata_delete(emd);
} else {
GtEncseqLoader *encseq_loader;
GtEncseq *encseq;
encseq_loader = gt_encseq_loader_new();
if (arguments->mirror)
gt_encseq_loader_mirror(encseq_loader);
if (!(encseq = gt_encseq_loader_load(encseq_loader,
argv[parsed_args], err)))
had_err = -1;
if (!had_err) {
const GtStrArray *filenames;
GtUword i;
if (!arguments->noindexname) {
gt_file_xprintf(arguments->outfp, "index name: ");
gt_file_xprintf(arguments->outfp, "%s\n", argv[parsed_args]);
}
gt_file_xprintf(arguments->outfp, "file format version: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n", gt_encseq_version(encseq));
gt_file_xprintf(arguments->outfp, "64-bit file: ");
gt_file_xprintf(arguments->outfp, "%s\n", gt_encseq_is_64_bit(encseq)
? "yes"
: "no");
gt_file_xprintf(arguments->outfp, "total length: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_total_length(encseq));
gt_file_xprintf(arguments->outfp, "compressed size: ");
gt_file_xprintf(arguments->outfp, ""GT_WU" bytes\n",
gt_encseq_sizeofrep(encseq));
gt_file_xprintf(arguments->outfp, "number of sequences: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_num_of_sequences(encseq));
gt_file_xprintf(arguments->outfp, "number of files: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_num_of_files(encseq));
gt_file_xprintf(arguments->outfp, "length of shortest/longest "
"sequence: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"/"GT_WU"\n",
gt_encseq_min_seq_length(encseq),
gt_encseq_max_seq_length(encseq));
filenames = gt_encseq_filenames(encseq);
gt_file_xprintf(arguments->outfp, "original filenames:\n");
for (i = 0; i < gt_str_array_size(filenames); i++) {
gt_file_xprintf(arguments->outfp, "\t%s ("GT_WU" characters)\n",
gt_str_array_get(filenames, i),
(GtUword)
gt_encseq_effective_filelength(encseq, i));
}
alpha = gt_encseq_alphabet(encseq);
chars = gt_alphabet_characters(alpha);
gt_file_xprintf(arguments->outfp, "alphabet size: ");
gt_file_xprintf(arguments->outfp, "%u\n",
gt_alphabet_num_of_chars(alpha));
gt_file_xprintf(arguments->outfp, "alphabet characters: ");
gt_file_xprintf(arguments->outfp, "%.*s", gt_alphabet_num_of_chars(alpha),
(char*) chars);
if (gt_alphabet_is_dna(alpha))
gt_file_xprintf(arguments->outfp, " (DNA)");
if (gt_alphabet_is_protein(alpha))
gt_file_xprintf(arguments->outfp, " (Protein)");
gt_file_xprintf(arguments->outfp, "\n");
if (arguments->show_alphabet) {
GtStr *out = gt_str_new();
gt_alphabet_to_str(alpha, out);
gt_file_xprintf(arguments->outfp, "alphabet definition:\n");
gt_file_xprintf(arguments->outfp, "%s\n", gt_str_get(out));
gt_str_delete(out);
}
gt_file_xprintf(arguments->outfp, "character distribution:\n");
for (i = 0; i < gt_alphabet_num_of_chars(alpha); i++) {
GtUword cc;
cc = gt_encseq_charcount(encseq, gt_alphabet_encode(alpha, chars[i]));
gt_file_xprintf(arguments->outfp, "\t%c: "GT_WU" (%.2f%%)\n",
(char) chars[i],
cc,
(cc /(double) (gt_encseq_total_length(encseq)
- gt_encseq_num_of_sequences(encseq)+1))*100);
}
gt_file_xprintf(arguments->outfp, "number of wildcards: ");
gt_file_xprintf(arguments->outfp, ""GT_WU" ("GT_WU" range(s))\n",
gt_encseq_wildcards(encseq),
gt_encseq_realwildcardranges(encseq));
gt_file_xprintf(arguments->outfp, "number of special characters: ");
gt_file_xprintf(arguments->outfp, ""GT_WU" ("GT_WU" range(s))\n",
gt_encseq_specialcharacters(encseq),
gt_encseq_realspecialranges(encseq));
gt_file_xprintf(arguments->outfp, "length of longest non-special "
"character stretch: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_lengthoflongestnonspecial(encseq));
gt_file_xprintf(arguments->outfp, "accesstype: ");
gt_file_xprintf(arguments->outfp, "%s\n",
gt_encseq_access_type_str(gt_encseq_accesstype_get(encseq)));
gt_file_xprintf(arguments->outfp, "bits used per character: ");
gt_file_xprintf(arguments->outfp, "%f\n",
(double) ((uint64_t) CHAR_BIT *
(uint64_t) gt_encseq_sizeofrep(encseq)) /
(double) gt_encseq_total_length(encseq));
gt_file_xprintf(arguments->outfp, "has special ranges: ");
gt_file_xprintf(arguments->outfp, "%s\n",
gt_encseq_has_specialranges(encseq)
? "yes"
: "no");
gt_file_xprintf(arguments->outfp, "has description support: ");
gt_file_xprintf(arguments->outfp, "%s\n",
gt_encseq_has_description_support(encseq)
? "yes"
: "no");
if (gt_encseq_has_description_support(encseq)) {
gt_file_xprintf(arguments->outfp, "length of longest description: ");
gt_file_xprintf(arguments->outfp, ""GT_WU"\n",
gt_encseq_max_desc_length(encseq));
}
gt_file_xprintf(arguments->outfp, "has multiple sequence support: ");
gt_file_xprintf(arguments->outfp, "%s\n",
gt_encseq_has_multiseq_support(encseq)
? "yes"
: "no");
}
gt_encseq_delete(encseq);
gt_encseq_loader_delete(encseq_loader);
}
return had_err;
}
