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add -r for stk_subseq to remove seq #133

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add -r for stk_subseq to remove seq #133

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95 changes: 62 additions & 33 deletions seqtk.c
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Original file line number Diff line number Diff line change
Expand Up @@ -548,18 +548,20 @@ int stk_subseq(int argc, char *argv[])
khash_t(reg) *h = kh_init(reg);
gzFile fp;
kseq_t *seq;
int l, i, j, c, is_tab = 0, line = 0;
int l, i, j, c, is_tab = 0, line = 0, remove = 0;
khint_t k;
while ((c = getopt(argc, argv, "tl:")) >= 0) {
while ((c = getopt(argc, argv, "trl:")) >= 0) {
switch (c) {
case 't': is_tab = 1; break;
case 'l': line = atoi(optarg); break;
case 't': is_tab = 1; break;
case 'r': remove = 1; break;
case 'l': line = atoi(optarg); break;
}
}
if (optind + 2 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk subseq [options] <in.fa> <in.bed>|<name.list>\n\n");
fprintf(stderr, "Options: -t TAB delimited output\n");
fprintf(stderr, " -r extract sequence that id is not in <in.bed>|<name.list>\n");
fprintf(stderr, " -l INT sequence line length [%d]\n\n", line);
fprintf(stderr, "Note: Use 'samtools faidx' if only a few regions are intended.\n\n");
return 1;
Expand All @@ -579,38 +581,65 @@ int stk_subseq(int argc, char *argv[])
while ((l = kseq_read(seq)) >= 0) {
reglist_t *p;
k = kh_get(reg, h, seq->name.s);
if (k == kh_end(h)) continue;
p = &kh_val(h, k);
for (i = 0; i < p->n; ++i) {
int beg = p->a[i]>>32, end = p->a[i];
if (beg >= seq->seq.l) {
fprintf(stderr, "[subseq] %s: %d >= %ld\n", seq->name.s, beg, seq->seq.l);
continue;
}
if (end > seq->seq.l) end = seq->seq.l;
if ((k == kh_end(h)) && (remove == 1)) {
if (is_tab == 0) {
printf("%c%s", seq->qual.l == seq->seq.l? '@' : '>', seq->name.s);
if (beg > 0 || (int)p->a[i] != INT_MAX) {
if (end == INT_MAX) {
if (beg) printf(":%d", beg+1);
} else printf(":%d-%d", beg+1, end);
if (seq->qual.l == seq->seq.l) {
printf("@%s", seq->name.s);
if (seq->comment.l) printf(" %s", seq->comment.s);
putchar('\n');
printf("%s\n", seq->seq.s);
printf("+\n");
printf("%s\n", seq->qual.s);
} else {
printf(">%s", seq->name.s);
if (seq->comment.l) printf(" %s", seq->comment.s);
for (j = 0; j < seq->seq.l; ++j) {
if ((j == 0) || (line > 0 && j % line == 0)) putchar('\n');
putchar(seq->seq.s[j]);
}
putchar('\n');
}
if (seq->comment.l) printf(" %s", seq->comment.s);
} else printf("%s\t%d\t", seq->name.s, beg + 1);
if (end > seq->seq.l) end = seq->seq.l;
for (j = 0; j < end - beg; ++j) {
if (is_tab == 0 && (j == 0 || (line > 0 && j % line == 0))) putchar('\n');
putchar(seq->seq.s[j + beg]);
}
putchar('\n');
if (seq->qual.l != seq->seq.l || is_tab) continue;
printf("+");
for (j = 0; j < end - beg; ++j) {
if (j == 0 || (line > 0 && j % line == 0)) putchar('\n');
putchar(seq->qual.s[j + beg]);
} else printf("%s\t1\t%s\n", seq->name.s, seq->seq.s);
} else {
if ((k == kh_end(h)) || (remove == 1)) continue;
p = &kh_val(h, k);
for (i = 0; i < p->n; ++i) {
int beg = p->a[i]>>32, end = p->a[i];
if (beg >= seq->seq.l) {
fprintf(stderr, "[subseq] %s: %d >= %ld\n", seq->name.s, beg, seq->seq.l);
continue;
}
if (end > seq->seq.l) end = seq->seq.l;
if (is_tab == 0) {
printf("%c%s", seq->qual.l == seq->seq.l? '@' : '>', seq->name.s);
if (beg > 0 || (int)p->a[i] != INT_MAX) {
if (end == INT_MAX) {
if (beg) printf(":%d", beg+1);
} else printf(":%d-%d", beg+1, end);
}
if (seq->comment.l) printf(" %s", seq->comment.s);
} else printf("%s\t%d\t", seq->name.s, beg + 1);
if (end > seq->seq.l) end = seq->seq.l;
if (seq->qual.l == seq->seq.l) {
if (is_tab == 0) putchar('\n');
for (j = 0; j < end - beg; ++j) {
putchar(seq->seq.s[j + beg]);
}
} else {
for (j = 0; j < end - beg; ++j) {
if ((is_tab == 0) && (j == 0 || (line > 0 && j % line == 0))) putchar('\n');
putchar(seq->seq.s[j + beg]);
}
}
putchar('\n');
if (seq->qual.l != seq->seq.l || is_tab) continue;
printf("+\n");
for (j = 0; j < end - beg; ++j) {
putchar(seq->qual.s[j + beg]);
}
putchar('\n');
}
putchar('\n');
}
}
}
// free
kseq_destroy(seq);
Expand Down