bool AceParser::parse(fnLytSeq* seqfn) {
//read all seqs and their positions from the file
//also checks for duplicate seqnames (just in case)
if (f!=stdin) seek(0);
ctgIDs.Clear();
//GHash<int> ctgIDs; //contig IDs, to make them unique!
//
off_t ctgpos;
numContigs=0;
while ((ctgpos=fskipTo("CO "))>=0) {
numContigs++;
LytCtgData* ctgdata=new LytCtgData(ctgpos);
char* p=ctgdata->readName(linebuf->chars()+3, ctgIDs);
if (p==NULL) {
GMessage("AceParser: error parsing contig name!\n");
return false;
}
int ctglen, numseqs;
//p must be after contig name within linebuf!
if (sscanf(p, "%d %d", &ctglen, &numseqs)!=2) {
GMessage("Error parsing contig len and seq count at:\n%s\n",
linebuf->chars());
}
ctgdata->len=ctglen;
ctgdata->numseqs = numseqs;
ctgdata->offs = 1;
int ctgidx=contigs.Add(ctgdata);
loadContig(ctgidx, seqfn, false);
} //while contigs
if (ctgpos==-2) return false; //parsing failed: line too long ?!?
contigs.setSorted(true);
return true;
}
bool LayoutParser::parse(fnLytSeq* seqfn) {
//read all seqs and their positions from the file
//also checks for duplicate seqnames (just in case)
if (f!=stdin) seek(0);
ctgIDs.Clear();
//GHash<int> ctgIDs; //contig IDs, to make them unique!
//
int ctgpos;
numContigs=0;
while ((ctgpos=fskipTo(">"))>=0) { //locate the contig line
numContigs++;
LytCtgData* ctgdata=new LytCtgData(ctgpos);
char* p=ctgdata->readName(linebuf->chars()+1, ctgIDs);
if (p==NULL) {
GMessage("LayoutParser: error parsing contig name:\n%s\n", linebuf->chars());
return false;
}
int ctg_lpos, ctg_rpos, numseqs;
//p must be after contig name within linebuf!
ctg_lpos=0;ctg_rpos=0;
if (sscanf(p, "%d %d %d", &numseqs, &ctg_lpos, &ctg_rpos)<1) {
GMessage("Error parsing contig len and seq count at:\n%s\n",
p);
return false;
}
//ctg_numSeqs=numseqs;
ctgdata->numseqs=numseqs;
ctgdata->rpos=ctg_rpos;
ctgdata->lpos=ctg_lpos;
ctgdata->len=ctg_rpos-ctg_lpos+1;
ctgdata->offs=ctg_lpos;
int ctgidx=contigs.Add(ctgdata);
//now look and load all the component sequences
loadContig(ctgidx, seqfn, false);
} //while lines
contigs.setSorted(true);
return true;
}
/*************************************************
Function:
loadUpdatedEdges
Description:
Loads contig information and masks some contigs according to setting.
Input:
1. graphfile: prefix of graph file
Output:
None.
Return:
None.
*************************************************/
void loadUpdatedEdges ( char * graphfile )
{
char c, name[256], line[1024];
int bal_ed, cvg;
FILE * fp, *out_fp;
Kmer from_kmer, to_kmer;
unsigned int num_ctgge, length, index = 0, num_kmer;
unsigned int i = 0, j;
int newIndex;
unsigned int * length_array, *flag_array, diff_len;
char * outfile = graphfile;
long long cvgSum = 0;
long long counter = 0;
unsigned int avg_arc_wt;
int ctg_short_cutoff;
float high_cvg_cutoff1, high_cvg_cutoff2, low_cvg_cutoff;
int cut_len;
//get overlaplen from *.preGraphBasic
sprintf ( name, "%s.preGraphBasic", graphfile );
fp = ckopen ( name, "r" );
while ( fgets ( line, sizeof ( line ), fp ) != NULL )
{
if ( line[0] == 'V' )
{
sscanf ( line + 6, "%d %c %d", &num_kmer, &c, &overlaplen );
fprintf ( stderr, "Kmer size: %d\n", overlaplen );
break;
}
}
cut_len = COMPATIBLE_MODE == 0 ? overlaplen : 0;
if ( ctg_short == 0 )
{
ctg_short = overlaplen + 2;
}
ctg_short_cutoff = 2 * overlaplen + 2 < 100 ? 100 : 0;
fclose ( fp );
sprintf ( name, "%s.updated.edge", graphfile );
fp = ckopen ( name, "r" );
sprintf ( name, "%s.newContigIndex", outfile );
out_fp = ckopen ( name, "w" );
while ( fgets ( line, sizeof ( line ), fp ) != NULL )
{
if ( line[0] == 'E' )
{
sscanf ( line + 5, "%d", &num_ctgge );
fprintf ( stderr, "There are %d edge(s) in edge file.\n", num_ctgge );
break;
}
}
index_array = ( unsigned int * ) ckalloc ( ( num_ctgge + 1 ) * sizeof ( unsigned int ) );
length_array = ( unsigned int * ) ckalloc ( ( num_ctgge + 1 ) * sizeof ( unsigned int ) );
flag_array = ( unsigned int * ) ckalloc ( ( num_ctgge + 1 ) * sizeof ( unsigned int ) );
while ( fgets ( line, sizeof ( line ), fp ) != NULL )
{
if ( line[0] == '>' )
{
sscanf ( line + 7, "%d", &length );
index_array[++index] = length;
length_array[++i] = length;
}
}
num_ctg = index;
orig2new = 1;
qsort ( & ( length_array[1] ), num_ctg, sizeof ( length_array[0] ), cmp_int );
//extract unique length
diff_len = 0;
for ( i = 1; i <= num_ctg; i++ )
{
for ( j = i + 1; j <= num_ctg; j++ )
if ( length_array[j] != length_array[i] )
{
break;
}
length_array[++diff_len] = length_array[i];
flag_array[diff_len] = i;
i = j - 1;
}
contig_array = ( CONTIG * ) ckalloc ( ( num_ctg + 1 ) * sizeof ( CONTIG ) );
//load edges
index = 0;
rewind ( fp );
while ( fgets ( line, sizeof ( line ), fp ) != NULL )
{
if ( line[0] == '>' )
{
sscanf ( line, ">length %u,%d,%d", &length, &bal_ed, &cvg );
newIndex = uniqueLenSearch ( length_array, flag_array, diff_len, length );
index_array[++index] = newIndex;
if ( length != 0 ) { contig_array[newIndex].length = length - cut_len; }
else { contig_array[newIndex].length = 0; }
contig_array[newIndex].bal_edge = bal_ed + 1;
contig_array[newIndex].downwardConnect = NULL;
contig_array[newIndex].mask = 0;
contig_array[newIndex].flag = 0;
contig_array[newIndex].arcs = NULL;
contig_array[newIndex].seq = NULL;
contig_array[newIndex].multi = 0;
contig_array[newIndex].inSubGraph = 0;
contig_array[newIndex].bubbleInScaff = 0;
contig_array[newIndex].cvg = cvg / 10;
if ( cvg && length > 100 )
{
counter += length - cut_len;
cvgSum += cvg * ( length - cut_len );
}
fprintf ( out_fp, "%d %d %d\n", index, newIndex, contig_array[newIndex].bal_edge );
}
}
if ( counter )
{
cvgAvg = cvgSum / counter / 10 > 2 ? cvgSum / counter / 10 : 3;
}
//mark repeats
int bal_i;
if ( maskRep )
{
high_cvg_cutoff1 = cvg_high * cvgAvg;
high_cvg_cutoff2 = cvg_high * cvgAvg * 0.8;
low_cvg_cutoff = cvg_low * cvgAvg;
counter = 0;
fprintf ( stderr, "Mask contigs with coverage lower than %.1f or higher than %.1f, and strict length %d.\n", low_cvg_cutoff, high_cvg_cutoff1, ctg_short_cutoff );
for ( i = 1; i <= num_ctg; i++ )
{
bal_i = getTwinCtg ( i );
if ( ( contig_array[i].cvg + contig_array[bal_i].cvg ) > 2 * high_cvg_cutoff1 )
{
contig_array[i].mask = 1;
contig_array[bal_i].mask = 1;
if ( i == bal_i ) { counter += 1; }
else { counter += 2; }
}
else if ( contig_array[i].length < ctg_short_cutoff && ( contig_array[i].cvg > high_cvg_cutoff2 || contig_array[bal_i].cvg > high_cvg_cutoff2 || ( contig_array[i].cvg < low_cvg_cutoff && contig_array[bal_i].cvg < low_cvg_cutoff ) ) )
{
contig_array[i].mask = 1;
contig_array[bal_i].mask = 1;
if ( i == bal_i ) { counter += 1; }
else { counter += 2; }
}
else if ( cvgAvg < 50 && ( contig_array[i].cvg >= 63 || contig_array[bal_i].cvg >= 63 ) )
{
contig_array[i].mask = 1;
contig_array[bal_i].mask = 1;
if ( i == bal_i ) { counter += 1; }
else { counter += 2; }
}
if ( isSmallerThanTwin ( i ) )
{
i++;
}
}
fprintf ( stderr, "Average contig coverage is %d, %lld contig(s) masked.\n", cvgAvg, counter );
}
counter = 0;
for ( i = 1; i <= num_ctg; i++ )
{
if ( contig_array[i].mask )
{
continue;
}
bal_i = getTwinCtg ( i );
if ( contig_array[i].length < ctg_short )
{
contig_array[i].mask = 1;
contig_array[bal_i].mask = 1;
if ( i == bal_i ) { counter += 1; }
else { counter += 2; }
}
if ( isSmallerThanTwin ( i ) )
{
i++;
}
}
fprintf ( stderr, "Mask contigs shorter than %d, %lld contig(s) masked.\n", ctg_short, counter );
avg_arc_wt = loadArcs ( graphfile );
counter = 0;
//counter = maskRepeatByArc(avg_arc_wt);
//printf ("Mask contigs with multi arcs, %d contig masked\n", counter);
//tipsCount();
loadContig ( graphfile );
fprintf ( stderr, "Done loading updated edges.\n" );
free ( ( void * ) length_array );
free ( ( void * ) flag_array );
fclose ( fp );
fclose ( out_fp );
}