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seqtk_telomere_reads_output #204

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9791287
Update seqtk.c
Wenfei-Xian Oct 18, 2023
88661cf
Update README.md
Wenfei-Xian Oct 18, 2023
9c141fb
Update README.md
Wenfei-Xian Oct 18, 2023
96eb70e
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Wenfei-Xian Oct 20, 2023
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3 changes: 2 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -61,4 +61,5 @@ Seqtk Examples

* Find telomere (TTAGGG)n repeats:

seqtk telo seq.fa > telo.bed 2> telo.count
seqtk telo seq.fa > telo.fasta
In this folk, the origin sequences will be output
13 changes: 11 additions & 2 deletions seqtk.c
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Expand Up @@ -2010,7 +2010,10 @@ int stk_telo(int argc, char *argv[])
else if (max - score > max_drop) break;
}
if (max >= min_score) {
if (!show_profile) printf("%s\t0\t%ld\t%ld\n", seq->name.s, max_i + 1, seq->seq.l);
if (!show_profile) printf(">%s\t0\t%ld\t%ld\n", seq->name.s, max_i + 1, seq->seq.l);
printf("%s\n", seq->seq.s);
if (!show_profile) printf(">%s_remove\t%ld\t%ld\t%ld\n", seq->name.s, max_i, seq->seq.l, seq->seq.l);
printf("%s\n", seq->seq.s + max_i + 1);
sum_telo += max_i + 1;
st = max_i + 1;
}
Expand All @@ -2028,7 +2031,13 @@ int stk_telo(int argc, char *argv[])
else if (max - score > max_drop) break;
}
if (max >= min_score) {
if (!show_profile) printf("%s\t%ld\t%ld\t%ld\n", seq->name.s, max_i, seq->seq.l, seq->seq.l);
if (!show_profile) printf(">%s\t%ld\t%ld\t%ld\n", seq->name.s, max_i, seq->seq.l, seq->seq.l);
printf("%s\n", seq->seq.s);
if (!show_profile) printf(">%s_remove\t%ld\t%ld\t%ld\n", seq->name.s, max_i, seq->seq.l, seq->seq.l);
char temp_char = seq->seq.s[max_i];
seq->seq.s[max_i] = '\0';
printf("%s\n", seq->seq.s);
seq->seq.s[max_i] = temp_char;
sum_telo += seq->seq.l - max_i;
}
}
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