// Deletes the front of the search bar and updates the search matcher
void do_del(){
del_letter();
/* Ignore the matcher if the string query is below the threshhold
Update and add matches when we delete letters */
if(qs_length() < SEARCH_THRESHHOLD){
draw_information_box("ENTER YOUR SEARCH!");
}
if(qs_length() >= SEARCH_THRESHHOLD){
add_matches();
}
}
static GtUword front_second_inplace(Frontvalue *midfront,
Frontvalue *lowfront,
GtUword history,
Sequenceobject *useq,
Sequenceobject *vseq)
{
GtUword alignedlen, maxalignedlen;
const uint64_t mask = ((uint64_t) 1) << (history-1);
*(lowfront+1) = *(lowfront+2) = *lowfront;
lowfront->row++;
lowfront->backreference = FT_EOP_DELETION;
UPDATE_MATCH_HISTORY(lowfront->matchhistory_count,lowfront->matchhistory);
add_matches(midfront,lowfront,mask,useq,vseq);
maxalignedlen = GT_MULT2(lowfront->row) + FRONT_DIAGONAL(lowfront);
(lowfront+1)->row++;
(lowfront+1)->backreference = FT_EOP_REPLACEMENT;
UPDATE_MATCH_HISTORY((lowfront+1)->matchhistory_count,
(lowfront+1)->matchhistory);
add_matches(midfront,lowfront + 1,mask,useq,vseq);
alignedlen = GT_MULT2((lowfront+1)->row) + FRONT_DIAGONAL(lowfront + 1);
if (maxalignedlen < alignedlen)
{
maxalignedlen = alignedlen;
}
(lowfront+2)->backreference = FT_EOP_INSERTION;
UPDATE_MATCH_HISTORY((lowfront+2)->matchhistory_count,
(lowfront+2)->matchhistory);
add_matches(midfront,lowfront + 2,mask,useq,vseq);
alignedlen = GT_MULT2((lowfront+2)->row) + FRONT_DIAGONAL(lowfront + 2);
if (maxalignedlen < alignedlen)
{
maxalignedlen = alignedlen;
}
return maxalignedlen;
}
// Draws the character on the search bar and updates the search matcher
void do_key(char key){
add_letter(key);
/* Ignore the matcher if the string query length is below the threshhold to provide matchings
Update and delete matches when we add letters */
if(qs_length() < SEARCH_THRESHHOLD){
draw_information_box("ENTER YOUR SEARCH!");
}
if(qs_length() > SEARCH_THRESHHOLD && MN_COUNT > 0){
del_matches();
}
if(qs_length() == SEARCH_THRESHHOLD){
add_matches();
}
}
int main(int argc, char **argv) {
char **fasta_files;
int seed_len, i, n_fasta_files;
ChrTable *chr_tab;
SeedTable *seed_tab;
Seq *seq;
gzFile gzf, out_gzf;
char *out_filename;
if(argc < 4) {
fprintf(stderr, "usage: %s <seed_len> <chromInfo.txt> "
"<output_seed_index.gz> [chr1.fa.gz [chr2.fa.gz [...]]]\n",
argv[0]);
exit(2);
}
seed_len = util_parse_long(argv[1]);
fasta_files = &argv[4];
n_fasta_files = argc - 4;
out_filename = argv[3];
/* read chromosomes and make table containing offsets for both
* forward and reverse strands (so we can represent genomic
* coordinates with a single long integer).
*/
chr_tab = chr_table_read(argv[2]);
fprintf(stderr, "there are %d chromosomes, total length: %u\n",
chr_tab->n_chr, chr_tab->total_chr_len);
/* create a table to hold seed matches */
fprintf(stderr, "initializing seed table\n");
seed_tab = seed_table_new(seed_len);
/* open an output file to write seed table to */
if(util_file_exists(out_filename)) {
my_err("output file %s already exists\n", out_filename);
exit(2);
}
out_gzf = util_must_gzopen(out_filename, "wb");
/*
* first pass: count number of matches to each seed
*/
seq = seq_new();
for(i = 0; i < n_fasta_files; i++) {
fprintf(stderr, "reading sequence from file %s\n", fasta_files[i]);
gzf = util_must_gzopen(fasta_files[i], "rb");
while(seq_read_fasta_record(seq, gzf)) {
fprintf(stderr, "%s %ld\n", seq->name, seq->len);
fprintf(stderr, "counting seed matches\n");
count_matches(chr_tab, seed_tab, seq);
}
gzclose(gzf);
}
/*
* second pass: store location of each match
*/
for(i = 0; i < n_fasta_files; i++) {
fprintf(stderr, "reading sequence from file %s\n", fasta_files[i]);
gzf = util_must_gzopen(fasta_files[i], "rb");
while(seq_read_fasta_record(seq, gzf)) {
fprintf(stderr, "%s %ld\n", seq->name, seq->len);
fprintf(stderr, "recording seed match positions\n");
add_matches(chr_tab, seed_tab, seq);
}
gzclose(gzf);
}
seq_free(seq);
/* write table to file in binary format */
fprintf(stderr, "writing seed table to file %s\n", out_filename);
seed_table_write(seed_tab, out_gzf);
gzclose(out_gzf);
chr_table_free(chr_tab);
seed_table_free(seed_tab);
return 0;
}
GtUword front_prune_edist_inplace(
#ifndef OUTSIDE_OF_GT
bool forward,
GtAllocatedMemory *frontspace,
#endif
Trimstat *trimstat,
Polished_point *best_polished_point,
Fronttrace *front_trace,
const Polishing_info *pol_info,
GtUword history,
GtUword minmatchnum,
GtUword maxalignedlendifference,
FTsequenceResources *ufsr,
GtUword ustart,
GtUword ulen,
FTsequenceResources *vfsr,
GtUword vstart,
GtUword vlen)
{
const GtUword sumseqlength = ulen + vlen,
minsizeforshift = sumseqlength/1000,
minlenforhistorycheck = GT_MULT2(history);
/* so the space for allocating the fronts is
sizeof (Frontvalue) * ((m+n)/1000 + maxvalid), where maxvalid is a small
constant. */
GtUword distance, trimleft = 0, valid = 1UL, maxvalid = 0, sumvalid = 0;
const uint64_t mask = ((uint64_t) 1) << (history-1);
Frontvalue *validbasefront;
bool diedout = false;
Sequenceobject useq, vseq;
#ifdef OUTSIDE_OF_GT
GtAllocatedMemory *frontspace = gt_malloc(sizeof *frontspace);
frontspace->space = NULL;
frontspace->allocated = 0;
frontspace->offset = 0;
sequenceobject_init(&useq,useqptr,ustart,ulen);
sequenceobject_init(&vseq,vseqptr,vstart,vlen);
#else
GtReadmode readmode = forward ? GT_READMODE_FORWARD : GT_READMODE_REVERSE;
sequenceobject_init(&useq,ufsr->extend_char_access,ufsr->encseq,readmode,
ustart,ulen,ufsr->encseq_r,ufsr->sequence_cache,
ufsr->totallength);
sequenceobject_init(&vseq,ufsr->extend_char_access,vfsr->encseq,readmode,
vstart,vlen,vfsr->encseq_r,vfsr->sequence_cache,
vfsr->totallength);
frontspace->offset = 0;
#endif
#ifdef TRIM_INFO_OUT
printf("regionalquality(minmatchnum)=" GT_WU "\n",minmatchnum);
#endif
for (distance = 0, valid = 1UL; /* Nothing */; distance++, valid += 2)
{
GtUword trim, maxalignedlen, minlenfrommaxdiff;
#ifdef TRIM_INFO_OUT
printf("distance=" GT_WU ",full=" GT_WU ",trimleft=" GT_WU
",valid=" GT_WU "\n",distance,
GT_MULT2(distance) + 1,
trimleft,valid);
#endif
gt_assert(valid <= GT_MULT2(distance) + 1);
sumvalid += valid;
if (maxvalid < valid)
{
maxvalid = valid;
}
validbasefront = frontspace_allocate(minsizeforshift,trimleft,valid,
frontspace);
if (distance == 0)
{
validbasefront->row = 0;
validbasefront->matchhistory = 0;
validbasefront->matchhistory_count = 0;
validbasefront->backreference = 0; /* No back reference */
add_matches(validbasefront + distance,validbasefront,mask,&useq,&vseq);
maxalignedlen = GT_MULT2(validbasefront->row);
} else
{
gt_assert(valid >= 3UL);
frontspace_check((const Frontvalue *) frontspace->space,
((const Frontvalue *) frontspace->space)
+ frontspace->allocated - 1,
validbasefront + trimleft);
frontspace_check((const Frontvalue *) frontspace->space,
((const Frontvalue *) frontspace->space)
+ frontspace->allocated - 1,
validbasefront + trimleft + valid - 1);
if (valid == 3UL)
{
maxalignedlen
= front_second_inplace(validbasefront + distance,
validbasefront + trimleft,
history,
&useq,
&vseq);
} else
{
maxalignedlen
= front_next_inplace(validbasefront + distance,
validbasefront + trimleft,
validbasefront + trimleft + valid - 1,
history,
&useq,
&vseq);
}
}
gt_assert(valid > 0);
minlenfrommaxdiff = maxalignedlen >= maxalignedlendifference
? maxalignedlen - maxalignedlendifference
: 0;
#ifdef TRIM_INFO_OUT
printf("maxalignedlen=" GT_WU ",maxlenfrommaxdiff=" GT_WU "\n",
maxalignedlen,minlenfrommaxdiff);
#endif
trim = trim_front(true,
#ifdef TRIM_INFO_OUT
distance,
#endif
ulen,
vlen,
minmatchnum,
minlenforhistorycheck,
minlenfrommaxdiff,
validbasefront + distance,
validbasefront + trimleft,
validbasefront + trimleft + valid);
#ifdef TRIM_INFO_OUT
printf("trim on left=" GT_WU "\n",trim);
#endif
if (trim > 0)
{
trimleft += trim;
gt_assert(valid >= trim);
valid -= trim;
}
if (valid > 0)
{
trim = trim_front(false,
#ifdef TRIM_INFO_OUT
distance,
#endif
ulen,
vlen,
minmatchnum,
minlenforhistorycheck,
minlenfrommaxdiff,
validbasefront + distance,
validbasefront + trimleft + valid - 1,
validbasefront + trimleft - 1);
#ifdef TRIM_INFO_OUT
printf("trim on right=" GT_WU "\n",trim);
#endif
gt_assert(trim < valid);
if (trim > 0)
{
gt_assert(valid >= trim);
valid -= trim;
}
}
if (valid == 0)
{
diedout = true;
break;
}
if (front_trace != NULL)
{
front_trace_add_gen(front_trace,trimleft,valid);
}
update_trace_and_polished(best_polished_point,
#ifndef OUTSIDE_OF_GT
&useq.min_access_pos,
&vseq.min_access_pos,
#endif
front_trace,
pol_info,
distance,
trimleft,
validbasefront + distance,
validbasefront + trimleft,
validbasefront + trimleft + valid - 1);
if ((vlen > ulen && vlen - ulen <= distance) ||
(vlen <= ulen && ulen - vlen <= distance))
{
if (distance + vlen - ulen >= trimleft &&
distance + vlen - ulen <= trimleft + valid - 1 &&
validbasefront[distance + vlen - ulen].row == ulen)
{
break;
}
}
if (distance >= sumseqlength)
{
break;
}
}
trimstat_add(trimstat,diedout,sumvalid,maxvalid,distance,
sizeof (Frontvalue) * frontspace->allocated,
#ifndef OUTSIDE_OF_GT
useq.sequence_cache != NULL &&
vseq.sequence_cache != NULL ? MAX(useq.sequence_cache->allocated,
vseq.sequence_cache->allocated)
: 0
#else
0
#endif
);
return diedout ? sumseqlength + 1 : distance;
}
static GtUword front_next_inplace(Frontvalue *midfront,
Frontvalue *lowfront,
Frontvalue *highfront,
GtUword history,
Sequenceobject *useq,
Sequenceobject *vseq)
{
GtUword alignedlen, maxalignedlen;
const uint64_t mask = ((uint64_t) 1) << (history-1);
Frontvalue bestfront, insertion_value, replacement_value, *frontptr;
insertion_value = *lowfront; /* from previous diag -(d-1) => -d => DELETION */
bestfront = insertion_value;
bestfront.row++;
UPDATE_MATCH_HISTORY(bestfront.matchhistory_count,bestfront.matchhistory);
*lowfront = bestfront;
lowfront->backreference = FT_EOP_DELETION;
add_matches(midfront,lowfront,mask,useq,vseq);
maxalignedlen = GT_MULT2(lowfront->row) + FRONT_DIAGONAL(lowfront);
replacement_value = *(lowfront+1);
if (bestfront.row < replacement_value.row + 1)
{
bestfront = replacement_value;
bestfront.backreference = FT_EOP_DELETION;
bestfront.row++;
UPDATE_MATCH_HISTORY(bestfront.matchhistory_count,bestfront.matchhistory);
} else
{
bestfront.backreference = FT_EOP_REPLACEMENT;
if (bestfront.row == replacement_value.row + 1)
{
bestfront.backreference |= FT_EOP_DELETION;
}
}
*(lowfront+1) = bestfront;
add_matches(midfront,lowfront + 1,mask,useq,vseq);
alignedlen = GT_MULT2((lowfront+1)->row) + FRONT_DIAGONAL(lowfront + 1);
if (maxalignedlen < alignedlen)
{
maxalignedlen = alignedlen;
}
for (frontptr = lowfront+2; frontptr <= highfront; frontptr++)
{
bestfront = insertion_value;
bestfront.backreference = FT_EOP_INSERTION;
if (frontptr <= highfront - 1)
{
if (bestfront.row < replacement_value.row + 1)
{
bestfront = replacement_value;
bestfront.backreference = FT_EOP_REPLACEMENT;
bestfront.row++;
} else
{
if (bestfront.row == replacement_value.row + 1)
{
bestfront.backreference |= FT_EOP_REPLACEMENT;
}
}
}
if (frontptr <= highfront - 2)
{
if (bestfront.row < frontptr->row + 1)
{
bestfront = *frontptr;
bestfront.backreference = FT_EOP_DELETION;
bestfront.row++;
} else
{
if (bestfront.row == frontptr->row + 1)
{
bestfront.backreference |= FT_EOP_DELETION;
}
}
}
UPDATE_MATCH_HISTORY(bestfront.matchhistory_count,bestfront.matchhistory);
if (frontptr < highfront)
{
insertion_value = replacement_value;
replacement_value = *frontptr;
}
*frontptr = bestfront;
add_matches(midfront,frontptr,mask,useq,vseq);
alignedlen = GT_MULT2(frontptr->row) + FRONT_DIAGONAL(frontptr);
if (maxalignedlen < alignedlen)
{
maxalignedlen = alignedlen;
}
}
return maxalignedlen;
}
bool MatchesProto::MergePartialFromCodedStream(
::google::protobuf::io::CodedInputStream* input) {
#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
::google::protobuf::uint32 tag;
while ((tag = input->ReadTag()) != 0) {
switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
// optional fixed64 imageLseq = 1;
case 1: {
if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
::google::protobuf::uint64, ::google::protobuf::internal::WireFormatLite::TYPE_FIXED64>(
input, &imagelseq_)));
set_has_imagelseq();
} else {
goto handle_uninterpreted;
}
if (input->ExpectTag(17)) goto parse_imageRseq;
break;
}
// optional fixed64 imageRseq = 2;
case 2: {
if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
parse_imageRseq:
DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
::google::protobuf::uint64, ::google::protobuf::internal::WireFormatLite::TYPE_FIXED64>(
input, &imagerseq_)));
set_has_imagerseq();
} else {
goto handle_uninterpreted;
}
if (input->ExpectTag(26)) goto parse_matches;
break;
}
// repeated .sfm.DMatches matches = 3;
case 3: {
if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
parse_matches:
DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
input, add_matches()));
} else {
goto handle_uninterpreted;
}
if (input->ExpectTag(26)) goto parse_matches;
if (input->ExpectAtEnd()) return true;
break;
}
default: {
handle_uninterpreted:
if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
return true;
}
DO_(::google::protobuf::internal::WireFormat::SkipField(
input, tag, mutable_unknown_fields()));
break;
}
}
}
return true;
#undef DO_
}
int main(int argc, char *argv[]) {
int r;
sd_journal *j = NULL;
unsigned line = 0;
bool need_seek = false;
sd_id128_t previous_boot_id;
bool previous_boot_id_valid = false;
bool have_pager;
log_parse_environment();
log_open();
r = parse_argv(argc, argv);
if (r <= 0)
goto finish;
if (arg_new_id128) {
r = generate_new_id128();
goto finish;
}
#ifdef HAVE_ACL
if (!arg_quiet && geteuid() != 0 && in_group("adm") <= 0)
log_warning("Showing user generated messages only. Users in the group 'adm' can see all messages. Pass -q to turn this message off.");
#endif
if (arg_directory)
r = sd_journal_open_directory(&j, arg_directory, 0);
else
r = sd_journal_open(&j, arg_local ? SD_JOURNAL_LOCAL_ONLY : 0);
if (r < 0) {
log_error("Failed to open journal: %s", strerror(-r));
goto finish;
}
if (arg_print_header) {
journal_print_header(j);
r = 0;
goto finish;
}
r = add_this_boot(j);
if (r < 0)
goto finish;
r = add_matches(j, argv + optind);
if (r < 0)
goto finish;
if (!arg_quiet) {
usec_t start, end;
char start_buf[FORMAT_TIMESTAMP_MAX], end_buf[FORMAT_TIMESTAMP_MAX];
r = sd_journal_get_cutoff_realtime_usec(j, &start, &end);
if (r < 0) {
log_error("Failed to get cutoff: %s", strerror(-r));
goto finish;
}
if (r > 0) {
if (arg_follow)
printf("Logs begin at %s.\n", format_timestamp(start_buf, sizeof(start_buf), start));
else
printf("Logs begin at %s, end at %s.\n",
format_timestamp(start_buf, sizeof(start_buf), start),
format_timestamp(end_buf, sizeof(end_buf), end));
}
}
if (arg_lines >= 0) {
r = sd_journal_seek_tail(j);
if (r < 0) {
log_error("Failed to seek to tail: %s", strerror(-r));
goto finish;
}
r = sd_journal_previous_skip(j, arg_lines);
} else {
r = sd_journal_seek_head(j);
if (r < 0) {
log_error("Failed to seek to head: %s", strerror(-r));
goto finish;
}
r = sd_journal_next(j);
}
if (r < 0) {
log_error("Failed to iterate through journal: %s", strerror(-r));
goto finish;
}
have_pager = !arg_no_pager && !arg_follow;
if (have_pager) {
columns();
pager_open();
}
if (arg_output == OUTPUT_JSON) {
fputc('[', stdout);
fflush(stdout);
}
for (;;) {
for (;;) {
sd_id128_t boot_id;
int flags = (arg_show_all*OUTPUT_SHOW_ALL |
have_pager*OUTPUT_FULL_WIDTH);
if (need_seek) {
r = sd_journal_next(j);
if (r < 0) {
log_error("Failed to iterate through journal: %s", strerror(-r));
goto finish;
}
}
if (r == 0)
break;
r = sd_journal_get_monotonic_usec(j, NULL, &boot_id);
if (r >= 0) {
if (previous_boot_id_valid &&
!sd_id128_equal(boot_id, previous_boot_id))
printf(ANSI_HIGHLIGHT_ON "----- Reboot -----" ANSI_HIGHLIGHT_OFF "\n");
previous_boot_id = boot_id;
previous_boot_id_valid = true;
}
line ++;
r = output_journal(j, arg_output, line, 0, flags);
if (r < 0)
goto finish;
need_seek = true;
}
if (!arg_follow)
break;
r = sd_journal_wait(j, (uint64_t) -1);
if (r < 0) {
log_error("Couldn't wait for log event: %s", strerror(-r));
goto finish;
}
}
if (arg_output == OUTPUT_JSON)
fputs("\n]\n", stdout);
finish:
if (j)
sd_journal_close(j);
pager_close();
return r < 0 ? EXIT_FAILURE : EXIT_SUCCESS;
}