/* Function: main()
* Synopsis: Run set of queries against an FM
* Purpose: Read in a FM and a file of query sequences.
* For each query, find matching FM interval, then collect positions in
* the original text T for the corresponding occurrences. These positions
* are 0-based (so first character is position 0).
*/
int
main(int argc, char *argv[])
{
void* tmp; // used for RALLOC calls
clock_t t1, t2;
struct tms ts1, ts2;
char *fname_fm = NULL;
char *fname_queries = NULL;
FM_HIT *hits = NULL;
char *line = NULL;
int status = eslOK;
int hit_cnt = 0;
int hit_indiv_cnt = 0;
int miss_cnt = 0;
int hit_num = 0;
int hit_num2 = 0;
int hits_size = 0;
int i,j;
int count_only = 0;
FM_INTERVAL interval;
FM_DATA *fmsf = NULL;
FM_DATA *fmsb = NULL;
FILE* fp_fm = NULL;
FILE* fp = NULL;
FILE* out = NULL;
char *outname = NULL;
ESL_GETOPTS *go = NULL; /* command line processing */
FM_CFG *cfg;
FM_METADATA *meta;
ESL_SQ *tmpseq; // used for sequence validation
ESL_ALPHABET *abc = NULL;
//start timer
t1 = times(&ts1);
process_commandline(argc, argv, &go, &fname_fm, &fname_queries);
if (esl_opt_IsOn(go, "--out")) {
outname = esl_opt_GetString(go, "--out");
if ( esl_strcmp ("-", outname) == 0 ) {
out = stdout;
outname = "stdout";
} else {
out = fopen(outname,"w");
}
}
if (esl_opt_IsOn(go, "--count_only"))
count_only = 1;
if((fp_fm = fopen(fname_fm, "rb")) == NULL)
esl_fatal("Cannot open file `%s': ", fname_fm);
fm_configAlloc(&cfg);
cfg->occCallCnt = 0;
meta = cfg->meta;
meta->fp = fp_fm;
fm_readFMmeta( meta);
if (meta->alph_type == fm_DNA) abc = esl_alphabet_Create(eslDNA);
else if (meta->alph_type == fm_AMINO) abc = esl_alphabet_Create(eslAMINO);
tmpseq = esl_sq_CreateDigital(abc);
//read in FM-index blocks
ESL_ALLOC(fmsf, meta->block_count * sizeof(FM_DATA) );
if (!meta->fwd_only)
ESL_ALLOC(fmsb, meta->block_count * sizeof(FM_DATA) );
for (i=0; i<meta->block_count; i++) {
fm_FM_read( fmsf+i,meta, TRUE );
if (!meta->fwd_only) {
fm_FM_read(fmsb+i, meta, FALSE );
fmsb[i].SA = fmsf[i].SA;
fmsb[i].T = fmsf[i].T;
}
}
fclose(fp_fm);
output_header(meta, stdout, go, fname_fm, fname_queries);
/* initialize a few global variables, then call initGlobals
* to do architecture-specific initialization
*/
fm_configInit(cfg, NULL);
fm_alphabetCreate(meta, NULL); // don't override charBits
fp = fopen(fname_queries,"r");
if (fp == NULL)
esl_fatal("Unable to open file %s\n", fname_queries);
ESL_ALLOC(line, FM_MAX_LINE * sizeof(char));
hits_size = 200;
ESL_ALLOC(hits, hits_size * sizeof(FM_HIT));
while(fgets(line, FM_MAX_LINE, fp) ) {
int qlen=0;
while (line[qlen] != '\0' && line[qlen] != '\n') qlen++;
if (line[qlen] == '\n') line[qlen] = '\0';
hit_num = 0;
for (i=0; i<meta->block_count; i++) {
fm_getSARangeReverse(fmsf+i, cfg, line, meta->inv_alph, &interval);
if (interval.lower>=0 && interval.lower <= interval.upper) {
int new_hit_num = interval.upper - interval.lower + 1;
hit_num += new_hit_num;
if (!count_only) {
if (hit_num > hits_size) {
hits_size = 2*hit_num;
ESL_RALLOC(hits, tmp, hits_size * sizeof(FM_HIT));
}
getFMHits(fmsf+i, cfg, &interval, i, hit_num-new_hit_num, qlen, hits, fm_forward);
}
}
/* find reverse hits, using backward search on the forward FM*/
if (!meta->fwd_only) {
fm_getSARangeForward(fmsb+i, cfg, line, meta->inv_alph, &interval);// yes, use the backward fm to produce the equivalent of a forward search on the forward fm
if (interval.lower>=0 && interval.lower <= interval.upper) {
int new_hit_num = interval.upper - interval.lower + 1;
hit_num += new_hit_num;
if (!count_only) {
if (hit_num > hits_size) {
hits_size = 2*hit_num;
ESL_RALLOC(hits, tmp, hits_size * sizeof(FM_HIT));
}
//even though I used fmsb above, use fmsf here, since we'll now do a backward trace
//in the FM-index to find the next sampled SA position
getFMHits(fmsf+i, cfg, &interval, i, hit_num-new_hit_num, qlen, hits, fm_backward);
}
}
}
}
if (hit_num > 0) {
if (count_only) {
hit_cnt++;
hit_indiv_cnt += hit_num;
} else {
hit_num2 = 0;
//for each hit, identify the sequence id and position within that sequence
for (i = 0; i< hit_num; i++) {
status = fm_getOriginalPosition (fmsf, meta, hits[i].block, hits[i].length, fm_forward, hits[i].start, &(hits[i].block), &(hits[i].start) );
hits[i].sortkey = (status==eslERANGE ? -1 : meta->seq_data[ hits[i].block ].target_id);
//validate match - if any characters in orig sequence were ambiguities, reject
fm_convertRange2DSQ( fmsf, meta, hits[i].start, hits[i].length, p7_NOCOMPLEMENT, tmpseq, TRUE );
for (j=1; j<=hits[i].length; j++) {
if (tmpseq->dsq[j] >= abc->K) {
hits[i].sortkey = -1; //reject
j = hits[i].length+1; //quit looking
}
}
if (hits[i].sortkey != -1)
hit_num2++; // legitimate hit
}
if (hit_num2 > 0)
hit_cnt++;
//now sort according the the sequence_id corresponding to that seq_offset
qsort(hits, hit_num, sizeof(FM_HIT), hit_sorter);
//skim past the skipped entries
i = 0;
while ( i < hit_num ) {
if (hits[i].sortkey != -1 )
break; //
i++;
}
if (i < hit_num) {
if (out != NULL) {
fprintf (out, "%s\n",line);
//fprintf (out, "\t%10s (%8d %s)\n",meta->seq_data[ hits[i].block ].name, hits[i].start, (hits[i].direction==fm_forward?"+":"-"));
fprintf (out, " %8ld %s %10s\n", (long)(hits[i].start), (hits[i].direction==fm_forward?"f":"r"), meta->seq_data[ hits[i].block ].name);
}
hit_indiv_cnt++;
i++; // skip the first one, since I'll be comparing each to the previous
for ( ; i< hit_num; i++) {
if ( //meta->seq_data[ hits[i].block ].id != meta->seq_data[ hits[i-1].block ].id ||
hits[i].sortkey != hits[i-1].sortkey || //sortkey is seq_data[].id
hits[i].direction != hits[i-1].direction ||
hits[i].start != hits[i-1].start )
{
if (out != NULL)
//fprintf (out, "\t%10s (%8d %s)\n",meta->seq_data[ hits[i].block ].name, hits[i].start, (hits[i].direction==fm_forward?"+":"-"));
fprintf (out, " %8ld %s %10s\n", (long)(hits[i].start), (hits[i].direction==fm_forward?"f":"r"), meta->seq_data[ hits[i].block ].name);
hit_indiv_cnt++;
}
}
if (out != NULL)
fprintf (out, "\n");
}
}
} else {
miss_cnt++;
}
}
for (i=0; i<meta->block_count; i++) {
fm_FM_destroy( fmsf+i, 1 );
if (!meta->fwd_only)
fm_FM_destroy( fmsb+i, 0 );
}
free (hits);
free (line);
fclose(fp);
fm_configDestroy(cfg);
// compute and print the elapsed time in millisec
t2 = times(&ts2);
{
double clk_ticks = sysconf(_SC_CLK_TCK);
double elapsedTime = (t2-t1)/clk_ticks;
double throughput = cfg->occCallCnt/elapsedTime;
fprintf (stderr, "hit: %-10d (%d)\n", hit_cnt, hit_indiv_cnt);
fprintf (stderr, "miss:%-10d\n", miss_cnt);
fprintf (stderr, "run time: %.2f seconds\n", elapsedTime);
fprintf (stderr, "occ calls: %12s\n", commaprint(cfg->occCallCnt));
fprintf (stderr, "occ/sec: %12s\n", commaprint(throughput));
}
exit(eslOK);
ERROR:
printf ("failure allocating memory for hits\n");
exit(status);
}
/* Function: main()
* Synopsis: break input sequence set into chunks, for each one building the
* Burrows-Wheeler transform and corresponding FM-index. Maintain requisite
* meta data.
* Notes: Currently depends on the divsufsort-lite code of Yuta Mori, though this
* could easily be replaced.
*/
int
main(int argc, char **argv)
{
char tmp_filename[16] = "fmtmpXXXXXX";
FILE *fptmp = NULL;
FILE *fp = NULL;
uint8_t *T = NULL;
uint8_t *BWT = NULL;
int *SA = NULL; //what I write will be 32-bit ints, but I need to keep this as int so it'll work with libdivsufsort
uint32_t *SAsamp = NULL;
uint32_t *occCnts_sb = NULL; // same indexing as above
uint32_t *cnts_sb = NULL;
uint16_t *occCnts_b = NULL; // this is logically a 2D array, but will be indexed as occ_cnts[alph_size*index + char] (instead of occ_cnts[index][char])
uint16_t *cnts_b = NULL;
FM_METADATA *meta = NULL;
clock_t t1, t2;
struct tms ts1, ts2;
long i,j,c;
int status = eslOK;
int chars_per_byte;
int num_freq_cnts_sb ;
int num_freq_cnts_b ;
int num_SA_samples ;
int infmt = eslSQFILE_UNKNOWN;
int alphatype = eslUNKNOWN;
int alphaguess =eslUNKNOWN;
ESL_ALPHABET *abc = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
ESL_SQ *tmpsq = NULL;
ESL_SQ_BLOCK *block = NULL;
char *fname_in = NULL;
char *fname_out= NULL;
int block_size = 50000000;
int sq_cnt = 0;
int use_tmpsq = 0;
uint64_t block_length;
uint64_t total_char_count = 0;
int max_block_size;
int numblocks = 0;
uint32_t numseqs = 0;
int allocedseqs = 1000;
uint32_t seq_offset = 0;
uint32_t ambig_offset = 0;
uint32_t overlap = 0;
uint16_t seq_cnt;
uint16_t ambig_cnt;
uint32_t prev_numseqs = 0;
int compressed_bytes;
uint32_t term_loc;
ESL_GETOPTS *go = NULL; /* command line processing */
uint8_t ambig_repl = 0;
int in_ambig_run = 0;
FM_AMBIGLIST ambig_list;
ESL_ALLOC (meta, sizeof(FM_METADATA));
if (meta == NULL)
esl_fatal("unable to allocate memory to store FM meta data\n");
ESL_ALLOC (meta->ambig_list, sizeof(FM_AMBIGLIST));
if (meta->ambig_list == NULL)
esl_fatal("unable to allocate memory to store FM ambiguity data\n");
fm_initAmbiguityList(meta->ambig_list);
meta->alph_type = fm_DNA;
meta->freq_SA = 8;
meta->freq_cnt_b = 256;
meta->freq_cnt_sb = pow(2,16); //65536 - that's the # values in a short
meta->seq_count = 0;
ESL_ALLOC (meta->seq_data, allocedseqs * sizeof(FM_SEQDATA));
if (meta->seq_data == NULL )
esl_fatal("unable to allocate memory to store FM sequence data\n");
process_commandline(argc, argv, &go, &fname_in, &fname_out);
if (esl_opt_IsOn(go, "--bin_length")) meta->freq_cnt_b = esl_opt_GetInteger(go, "--bin_length");
if ( meta->freq_cnt_b < 32 || meta->freq_cnt_b >4096 || (meta->freq_cnt_b & (meta->freq_cnt_b - 1)) ) // test power of 2
esl_fatal("bin_length must be a power of 2, at least 128, and at most 4096\n");
if (esl_opt_IsOn(go, "--sa_freq")) meta->freq_SA = esl_opt_GetInteger(go, "--sa_freq");
if ( (meta->freq_SA & (meta->freq_SA - 1)) ) // test power of 2
esl_fatal ("SA_freq must be a power of 2\n");
if (esl_opt_IsOn(go, "--block_size")) block_size = 1000000 * esl_opt_GetInteger(go, "--block_size");
if ( block_size <=0 )
esl_fatal ("block_size must be a positive number\n");
//start timer
t1 = times(&ts1);
output_header(stdout, go, fname_in, fname_out);
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat");
}
status = esl_sqfile_Open(fname_in, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file %s", fname_in);
else if (status == eslEFORMAT) esl_fatal("Format of seqfile %s unrecognized.", fname_in);
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
meta->fwd_only = 0;
if (esl_opt_IsUsed(go, "--alph")) {
meta->alph = esl_opt_GetString(go, "--alph") ;
if ( esl_strcmp(meta->alph, "dna")==0 || esl_strcmp(meta->alph, "rna")==0) {
meta->alph_type = fm_DNA;
alphatype = eslDNA;
} else if (esl_strcmp(meta->alph, "dna_full")==0 || esl_strcmp(meta->alph, "rna_full")==0) {
meta->alph_type = fm_DNA_full;
alphatype = eslDNA;
} else if (esl_strcmp(meta->alph, "amino")==0) {
meta->alph_type = fm_AMINO;
alphatype = eslAMINO;
meta->fwd_only = 1;
} else {
esl_fatal("Unknown alphabet type. Try 'dna', 'dna_full', or 'amino'\n%s", "");
}
} else {
esl_sqfile_GuessAlphabet(sqfp, &alphaguess);
if (alphaguess == eslDNA || alphaguess == eslRNA) {
meta->alph_type = fm_DNA;
alphatype = eslDNA;
} else if (alphaguess == eslAMINO) {
meta->alph_type = fm_AMINO;
alphatype = eslAMINO;
meta->fwd_only = 1;
} else {
esl_fatal("Unknown alphabet type. Try 'dna', 'dna_full', or 'amino'\n%s", "");
}
}
if (esl_opt_IsOn(go, "--fwd_only") )
meta->fwd_only = 1;
meta->alph = NULL;
//getInverseAlphabet
fm_alphabetCreate(meta, &(meta->charBits));
chars_per_byte = 8/meta->charBits;
//shift inv_alph up one, to make space for '$' at 0
for (i=0; i<256; i++)
if ( meta->inv_alph[i] >= 0)
meta->inv_alph[i]++;
abc = esl_alphabet_Create(alphatype);
sq = esl_sq_CreateDigital(abc);
tmpsq = esl_sq_CreateDigital(abc);
esl_sqfile_SetDigital(sqfp, abc);
block = esl_sq_CreateDigitalBlock(FM_BLOCK_COUNT, abc);
block->complete = FALSE;
// max_block_size = FM_BLOCK_OVERLAP+block_size+1 + block_size*.2; // +1 for the '$'
max_block_size = FM_BLOCK_OVERLAP+block_size+1 + block_size; // temporary hack to avoid memory over-runs (see end of 1101_fmindex_benchmarking/00NOTES)
if (alphatype == fm_DNA)
fm_initAmbiguityList(&ambig_list);
/* Allocate BWT, Text, SA, and FM-index data structures, allowing storage of maximally large sequence*/
ESL_ALLOC (T, max_block_size * sizeof(uint8_t));
ESL_ALLOC (BWT, max_block_size * sizeof(uint8_t));
ESL_ALLOC (SA, max_block_size * sizeof(int));
ESL_ALLOC (SAsamp, (1+floor((double)max_block_size/meta->freq_SA) ) * sizeof(uint32_t));
ESL_ALLOC (occCnts_sb, (1+ceil((double)max_block_size/meta->freq_cnt_sb)) * meta->alph_size * sizeof(uint32_t)); // every freq_cnt_sb positions, store an array of ints
ESL_ALLOC (cnts_sb, meta->alph_size * sizeof(uint32_t));
ESL_ALLOC (occCnts_b, ( 1+ceil((double)max_block_size/meta->freq_cnt_b)) * meta->alph_size * sizeof(uint16_t)); // every freq_cnt_b positions, store an array of 8-byte ints
ESL_ALLOC (cnts_b, meta->alph_size * sizeof(uint16_t));
if((T == NULL) || (BWT == NULL) || (SA==NULL) || (SAsamp==NULL) || (BWT==NULL) || (cnts_b==NULL) || (occCnts_b==NULL) || (cnts_sb==NULL) || (occCnts_sb==NULL) ) {
esl_fatal( "%s: Cannot allocate memory.\n", argv[0]);
}
// Open a temporary file, to which FM-index data will be written
if (esl_tmpfile(tmp_filename, &fptmp) != eslOK) esl_fatal("unable to open fm-index tmpfile");
/* Main loop: */
while (status == eslOK ) {
//reset block as an empty vessel
for (i=0; i<block->count; i++)
esl_sq_Reuse(block->list + i);
if (use_tmpsq) {
esl_sq_Copy(tmpsq , block->list);
block->complete = FALSE; //this lets ReadBlock know that it needs to append to a small bit of previously-read seqeunce
block->list->C = FM_BLOCK_OVERLAP; // overload the ->C value, which ReadBlock uses to determine how much
// overlap should be retained in the ReadWindow step
} else {
block->complete = TRUE;
}
status = esl_sqio_ReadBlock(sqfp, block, block_size, -1, alphatype != eslAMINO);
if (status == eslEOF) continue;
if (status != eslOK) ESL_XEXCEPTION(status, "failure reading sequence block");
seq_offset = numseqs;
ambig_offset = meta->ambig_list->count;
if (block->complete || block->count == 0) {
use_tmpsq = FALSE;
} else {
/* The final sequence on the block was a probably-incomplete window of the active sequence.
* Grab a copy of the end for use in the next pass, to ensure we don't miss hits crossing
* the boundary between two blocks.
*/
esl_sq_Copy(block->list + (block->count - 1) , tmpsq);
use_tmpsq = TRUE;
}
block->first_seqidx = sq_cnt;
sq_cnt += block->count - (use_tmpsq ? 1 : 0);// if there's an incomplete sequence read into the block wait to count it until it's complete.
/* Read dseqs from block into text element T.
* Convert the dsq from esl-alphabet to fm-alphabet (1..k for alphabet of size k).
* (a) collapsing upper/lower case for appropriate sorting.
* (b) reserving 0 for '$', which must be lexicographically smallest
* (these will later be shifted to 0-based alphabet, once SA has been built)
*
*/
block_length = 0;
for (i=0; i<block->count; i++) {
//start a new block, with space for the name
allocateSeqdata(meta, block->list+i, numseqs, &allocedseqs);
//meta data
meta->seq_data[numseqs].target_id = block->first_seqidx + i ;
meta->seq_data[numseqs].target_start = block->list[i].start;
meta->seq_data[numseqs].fm_start = block_length;
if (block->list[i].name == NULL) meta->seq_data[numseqs].name[0] = '\0';
else strcpy(meta->seq_data[numseqs].name, block->list[i].name );
if (block->list[i].acc == NULL) meta->seq_data[numseqs].acc[0] = '\0';
else strcpy(meta->seq_data[numseqs].acc, block->list[i].acc );
if (block->list[i].source == NULL) meta->seq_data[numseqs].source[0] = '\0';
else strcpy(meta->seq_data[numseqs].source, block->list[i].source );
if (block->list[i].desc == NULL) meta->seq_data[numseqs].desc[0] = '\0';
else strcpy(meta->seq_data[numseqs].desc, block->list[i].desc );
for (j=1; j<=block->list[i].n; j++) {
c = abc->sym[block->list[i].dsq[j]];
if ( meta->alph_type == fm_DNA) {
if (meta->inv_alph[c] == -1) {
// replace ambiguity characters by rotating through A,C,G, and T.
c = meta->alph[ambig_repl];
ambig_repl = (ambig_repl+1)%4;
if (!in_ambig_run) {
fm_addAmbiguityRange(meta->ambig_list, block_length, block_length);
in_ambig_run=1;
} else {
meta->ambig_list->ranges[meta->ambig_list->count - 1].upper = block_length;
}
} else {
in_ambig_run=0;
}
} else if (meta->inv_alph[c] == -1) {
esl_fatal("requested alphabet doesn't match input text\n");
}
T[block_length] = meta->inv_alph[c];
block_length++;
if (j>block->list[i].C) total_char_count++; // add to total count, only if it's not redundant with earlier read
meta->seq_data[numseqs].length++;
}
numseqs++;
}
T[block_length] = 0; // last character 0 is effectively '$' for suffix array
block_length++;
seq_cnt = numseqs-seq_offset;
ambig_cnt = meta->ambig_list->count - ambig_offset;
//build and write FM-index for T. This will be a BWT on the reverse of the sequence, required for reverse-traversal of the BWT
buildAndWriteFMIndex(meta, seq_offset, ambig_offset, seq_cnt, ambig_cnt, (uint32_t)block->list[0].C, T, BWT, SA, SAsamp,
occCnts_sb, cnts_sb, occCnts_b, cnts_b, block_length, fptmp);
if ( ! meta->fwd_only ) {
//build and write FM-index for un-reversed T (used to find reverse hits using forward traversal of the BWT
buildAndWriteFMIndex(meta, seq_offset, ambig_offset, seq_cnt, ambig_cnt, 0, T, BWT, SA, NULL,
occCnts_sb, cnts_sb, occCnts_b, cnts_b, block_length, fptmp);
}
prev_numseqs = numseqs;
numblocks++;
}
esl_sqfile_Close(sqfp);
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
esl_sq_Destroy(tmpsq);
esl_sq_DestroyBlock(block);
meta->seq_count = numseqs;
meta->block_count = numblocks;
/* Finished writing the FM-index data to a temporary file. Now write
* metadata to fname_out, than append FM-index data from temp file
*/
if((fp = fopen(fname_out, "wb")) == NULL)
esl_fatal( "%s: Cannot open file `%s': ", argv[0], fname_out);
//write out meta data
if( fwrite(&(meta->fwd_only), sizeof(meta->fwd_only), 1, fp) != 1 ||
fwrite(&(meta->alph_type), sizeof(meta->alph_type), 1, fp) != 1 ||
fwrite(&(meta->alph_size), sizeof(meta->alph_size), 1, fp) != 1 ||
fwrite(&(meta->charBits), sizeof(meta->charBits), 1, fp) != 1 ||
fwrite(&(meta->freq_SA), sizeof(meta->freq_SA), 1, fp) != 1 ||
fwrite(&(meta->freq_cnt_sb), sizeof(meta->freq_cnt_sb), 1, fp) != 1 ||
fwrite(&(meta->freq_cnt_b), sizeof(meta->freq_cnt_b), 1, fp) != 1 ||
fwrite(&(meta->block_count), sizeof(meta->block_count), 1, fp) != 1 ||
fwrite(&(meta->seq_count), sizeof(meta->seq_count), 1, fp) != 1 ||
fwrite(&(meta->ambig_list->count), sizeof(meta->ambig_list->count), 1, fp) != 1 ||
fwrite(&total_char_count, sizeof(total_char_count), 1, fp) != 1
)
esl_fatal( "%s: Error writing meta data for FM index.\n", argv[0]);
for (i=0; i<meta->seq_count; i++) {
if( fwrite(&(meta->seq_data[i].target_id), sizeof(meta->seq_data[i].target_id), 1, fp) != 1 ||
fwrite(&(meta->seq_data[i].target_start), sizeof(meta->seq_data[i].target_start), 1, fp) != 1 ||
fwrite(&(meta->seq_data[i].fm_start), sizeof(meta->seq_data[i].fm_start), 1, fp) != 1 ||
fwrite(&(meta->seq_data[i].length), sizeof(meta->seq_data[i].length), 1, fp) != 1 ||
fwrite(&(meta->seq_data[i].name_length), sizeof(meta->seq_data[i].name_length), 1, fp) != 1 ||
fwrite(&(meta->seq_data[i].acc_length), sizeof(meta->seq_data[i].acc_length), 1, fp) != 1 ||
fwrite(&(meta->seq_data[i].source_length),sizeof(meta->seq_data[i].source_length), 1, fp) != 1 ||
fwrite(&(meta->seq_data[i].desc_length), sizeof(meta->seq_data[i].desc_length), 1, fp) != 1 ||
fwrite(meta->seq_data[i].name, sizeof(char), meta->seq_data[i].name_length+1 , fp) != meta->seq_data[i].name_length+1 ||
fwrite(meta->seq_data[i].acc, sizeof(char), meta->seq_data[i].acc_length+1 , fp) != meta->seq_data[i].acc_length+1 ||
fwrite(meta->seq_data[i].source, sizeof(char), meta->seq_data[i].source_length+1, fp) != meta->seq_data[i].source_length+1 ||
fwrite(meta->seq_data[i].desc, sizeof(char), meta->seq_data[i].desc_length+1 , fp) != meta->seq_data[i].desc_length+1
)
esl_fatal( "%s: Error writing meta data for FM index.\n", argv[0]);
}
for (i=0; i<meta->ambig_list->count; i++) {
if( fwrite(&(meta->ambig_list->ranges[i].lower), sizeof(meta->ambig_list->ranges[i].lower), 1, fp) != 1 ||
fwrite(&(meta->ambig_list->ranges[i].upper), sizeof(meta->ambig_list->ranges[i].upper), 1, fp) != 1
)
esl_fatal( "%s: Error writing ambiguity data for FM index.\n", argv[0]);
}
/* now append the FM-index data in fptmp to the desired output file, fp */
rewind(fptmp);
for (i=0; i<numblocks; i++) {
for(j=0; j< (meta->fwd_only?1:2); j++ ) { //do this once or twice, once for forward-T index, and possibly once for reversed
//first, read
if(fread(&block_length, sizeof(block_length), 1, fptmp) != 1)
esl_fatal( "%s: Error reading block_length in FM index.\n", argv[0]);
if(fread(&term_loc, sizeof(term_loc), 1, fptmp) != 1)
esl_fatal( "%s: Error reading terminal location in FM index.\n", argv[0]);
if(fread(&seq_offset, sizeof(seq_offset), 1, fptmp) != 1)
esl_fatal( "%s: Error reading seq_offset in FM index.\n", argv[0]);
if(fread(&ambig_offset, sizeof(ambig_offset ), 1, fptmp) != 1)
esl_fatal( "%s: Error reading ambig_offset in FM index.\n", argv[0]);
if(fread(&overlap, sizeof(overlap), 1, fptmp) != 1)
esl_fatal( "%s: Error reading overlap in FM index.\n", argv[0]);
if(fread(&seq_cnt, sizeof(seq_cnt), 1, fptmp) != 1)
esl_fatal( "%s: Error reading seq_cnt in FM index.\n", argv[0]);
if(fread(&ambig_cnt, sizeof(ambig_cnt), 1, fptmp) != 1)
esl_fatal( "%s: Error reading ambig_cnt in FM index.\n", argv[0]);
compressed_bytes = ((chars_per_byte-1+block_length)/chars_per_byte);
num_freq_cnts_b = 1+ceil((double)block_length/meta->freq_cnt_b);
num_freq_cnts_sb = 1+ceil((double)block_length/meta->freq_cnt_sb);
num_SA_samples = 1+floor((double)block_length/meta->freq_SA);
//j==0 test cause T and SA to be written only for forward sequence
if(j==0 && fread(T, sizeof(uint8_t), compressed_bytes, fptmp) != compressed_bytes)
esl_fatal( "%s: Error reading T in FM index.\n", argv[0]);
if(fread(BWT, sizeof(uint8_t), compressed_bytes, fptmp) != compressed_bytes)
esl_fatal( "%s: Error reading BWT in FM index.\n", argv[0]);
if(j==0 && fread(SAsamp, sizeof(uint32_t), (size_t)num_SA_samples, fptmp) != (size_t)num_SA_samples)
esl_fatal( "%s: Error reading SA in FM index.\n", argv[0]);
if(fread(occCnts_b, sizeof(uint16_t)*(meta->alph_size), (size_t)num_freq_cnts_b, fptmp) != (size_t)num_freq_cnts_b)
esl_fatal( "%s: Error reading occCnts_b in FM index.\n", argv[0]);
if(fread(occCnts_sb, sizeof(uint32_t)*(meta->alph_size), (size_t)num_freq_cnts_sb, fptmp) != (size_t)num_freq_cnts_sb)
esl_fatal( "%s: Error reading occCnts_sb in FM index.\n", argv[0]);
//then, write
if(fwrite(&block_length, sizeof(block_length), 1, fp) != 1)
esl_fatal( "%s: Error writing block_length in FM index.\n", argv[0]);
if(fwrite(&term_loc, sizeof(term_loc), 1, fp) != 1)
esl_fatal( "%s: Error writing terminal location in FM index.\n", argv[0]);
if(fwrite(&seq_offset, sizeof(seq_offset), 1, fp) != 1)
esl_fatal( "%s: Error writing seq_offset in FM index.\n", argv[0]);
if(fwrite(&ambig_offset, sizeof(ambig_offset), 1, fp) != 1)
esl_fatal( "%s: Error writing ambig_offset in FM index.\n", argv[0]);
if(fwrite(&overlap, sizeof(overlap), 1, fp) != 1)
esl_fatal( "%s: Error writing overlap in FM index.\n", argv[0]);
if(fwrite(&seq_cnt, sizeof(seq_cnt), 1, fp) != 1)
esl_fatal( "%s: Error writing seq_cnt in FM index.\n", argv[0]);
if(fwrite(&ambig_cnt, sizeof(ambig_cnt), 1, fp) != 1)
esl_fatal( "%s: Error writing ambig_cnt in FM index.\n", argv[0]);
if(j==0 && fwrite(T, sizeof(uint8_t), compressed_bytes, fp) != compressed_bytes)
esl_fatal( "%s: Error writing T in FM index.\n", argv[0]);
if(fwrite(BWT, sizeof(uint8_t), compressed_bytes, fp) != compressed_bytes)
esl_fatal( "%s: Error writing BWT in FM index.\n", argv[0]);
if(j==0 && fwrite(SAsamp, sizeof(uint32_t), (size_t)num_SA_samples, fp) != (size_t)num_SA_samples)
esl_fatal( "%s: Error writing SA in FM index.\n", argv[0]);
if(fwrite(occCnts_b, sizeof(uint16_t)*(meta->alph_size), (size_t)num_freq_cnts_b, fp) != (size_t)num_freq_cnts_b)
esl_fatal( "%s: Error writing occCnts_b in FM index.\n", argv[0]);
if(fwrite(occCnts_sb, sizeof(uint32_t)*(meta->alph_size), (size_t)num_freq_cnts_sb, fp) != (size_t)num_freq_cnts_sb)
esl_fatal( "%s: Error writing occCnts_sb in FM index.\n", argv[0]);
}
}
fprintf (stderr, "Number of characters in index: %ld\n", (long)total_char_count);
fprintf (stderr, "Number of FM-index blocks: %ld\n", (long)meta->block_count);
fclose(fp);
fclose(fptmp);
free(T);
free(BWT);
free(SA);
free(SAsamp);
free(occCnts_b);
free(cnts_b);
free(occCnts_sb);
free(cnts_sb);
fm_metaDestroy(meta);
esl_getopts_Destroy(go);
// compute and print the elapsed time in millisec
t2 = times(&ts2);
{
double clk_ticks = sysconf(_SC_CLK_TCK);
double elapsedTime = (t2-t1)/clk_ticks;
fprintf (stderr, "run time: %.2f seconds\n", elapsedTime);
}
return (eslOK);
ERROR:
/* Deallocate memory. */
if (fp) fclose(fp);
if (T) free(T);
if (BWT) free(BWT);
if (SA) free(SA);
if (SAsamp) free(SAsamp);
if (occCnts_b) free(occCnts_b);
if (cnts_b) free(cnts_b);
if (occCnts_sb) free(occCnts_sb);
if (cnts_sb) free(cnts_sb);
if (ambig_list.ranges) free(ambig_list.ranges);
fm_metaDestroy(meta);
esl_getopts_Destroy(go);
esl_sqfile_Close(sqfp);
esl_alphabet_Destroy(abc);
esl_sq_Destroy(sq);
if (tmpsq) esl_sq_Destroy(tmpsq);
if (block) esl_sq_DestroyBlock(block);
fprintf (stderr, "failure during memory allocation\n");
exit(status);
}
