Hello,
Can anyone decipher this code for me..
} else if(cat >= 2) {
if(lc != -1 && off == 0) off++;
lc = -1;
off++; // skip over gap character and increment
} else if(c == '>') {
if(off > 0 && lastc == '>') {
cerr << "Warning: Encountered reference sequence with only gaps" << endl;
} else if(lastc == '>') {
cerr << "Warning: Encountered empty reference sequence" << endl;
}
lastc = '>';
//return RefRecord(off, 0, false);
return RefRecord((uint32_t)off, 0, first);
}
c = in.get();
if(c == -1) {
// End-of-file
if(off > 0 && lastc == '>') {
cerr << "Warning: Encountered reference sequence with only gaps" << endl;
} else if(lastc == '>') {
cerr << "Warning: Encountered empty reference sequence" << endl;
}
lastc = -1;
//return RefRecord(off, 0, false);
return RefRecord((uint32_t)off, 0, first);
}
}
assert(!rparms.color || (lc != -1));
assert_eq(1, asc2dnacat[c]); // C must be unambiguous base
if(off > 0 && rparms.color && first) {
// Handle the case where the first record has ambiguous
// characters but we're in color space; one of those counts is
// spurious
off--;
}
I'm trying to build a bowtie index on a genome file but it returns the warning
"Encountered reference sequence with gaps".
I'm not sure what that means. My genome is not Rep Masked to have N (at least that I know of). And when I do downstream aligning only 20% of my reads aligns with the genome. When I created an index for an older version of the genome I did not encounter these warnings and I had more reads aligning to the genome (more than 50%). I am limited to using the new version of the genome since I am using a pipeline and the gff file I use later in the pipeline have the same headers as the new version of the genome.
My question is
1. What does the warning "encountered....." mean and how do I solve the issue?
2. Can the low percentage of reads aligning to the genome be because of these warnings?
Thanks in advance for your help!
Can anyone decipher this code for me..
} else if(cat >= 2) {
if(lc != -1 && off == 0) off++;
lc = -1;
off++; // skip over gap character and increment
} else if(c == '>') {
if(off > 0 && lastc == '>') {
cerr << "Warning: Encountered reference sequence with only gaps" << endl;
} else if(lastc == '>') {
cerr << "Warning: Encountered empty reference sequence" << endl;
}
lastc = '>';
//return RefRecord(off, 0, false);
return RefRecord((uint32_t)off, 0, first);
}
c = in.get();
if(c == -1) {
// End-of-file
if(off > 0 && lastc == '>') {
cerr << "Warning: Encountered reference sequence with only gaps" << endl;
} else if(lastc == '>') {
cerr << "Warning: Encountered empty reference sequence" << endl;
}
lastc = -1;
//return RefRecord(off, 0, false);
return RefRecord((uint32_t)off, 0, first);
}
}
assert(!rparms.color || (lc != -1));
assert_eq(1, asc2dnacat[c]); // C must be unambiguous base
if(off > 0 && rparms.color && first) {
// Handle the case where the first record has ambiguous
// characters but we're in color space; one of those counts is
// spurious
off--;
}
I'm trying to build a bowtie index on a genome file but it returns the warning
"Encountered reference sequence with gaps".
I'm not sure what that means. My genome is not Rep Masked to have N (at least that I know of). And when I do downstream aligning only 20% of my reads aligns with the genome. When I created an index for an older version of the genome I did not encounter these warnings and I had more reads aligning to the genome (more than 50%). I am limited to using the new version of the genome since I am using a pipeline and the gff file I use later in the pipeline have the same headers as the new version of the genome.
My question is
1. What does the warning "encountered....." mean and how do I solve the issue?
2. Can the low percentage of reads aligning to the genome be because of these warnings?
Thanks in advance for your help!