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improved help message

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lh3 committed Mar 24, 2012
1 parent efab340 commit 90324c42b5aabc5da9949c8997e631fe2d73c169
Showing with 9 additions and 2 deletions.
  1. +4 −0 .gitignore
  2. +5 −2 seqtk.c
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@@ -0,0 +1,4 @@
+*.o
+*.a
+*.dSYM
+.*.swp
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@@ -414,9 +414,10 @@ int stk_maskseq(int argc, char *argv[])
}
}
if (argc - optind < 2) {
+ fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk maskseq [-cl] <in.fa> <in.bed>\n\n");
fprintf(stderr, "Options: -c mask the complement regions\n");
- fprintf(stderr, " -l soft mask (to lower cases)\n");
+ fprintf(stderr, " -l soft mask (to lowercases)\n\n");
return 1;
}
h = stk_reg_read(argv[optind+1]);
@@ -486,7 +487,7 @@ int stk_subseq(int argc, char *argv[])
}
if (optind + 2 > argc) {
fprintf(stderr, "\n");
- fprintf(stderr, "Usage: seqtk subseq [-t] [-l lineLen=%d] <in.fa> <in.bed>|<name.list>\n\n", line);
+ fprintf(stderr, "Usage: seqtk subseq [options] <in.fa> <in.bed>|<name.list>\n\n");
fprintf(stderr, "Options: -t TAB delimited output\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");
@@ -915,6 +916,8 @@ int stk_sample(int argc, char *argv[])
return 0;
}
+/* seq */
+
int stk_seq(int argc, char *argv[])
{
gzFile fp;

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