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r41: print version number; added license
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lh3 committed Nov 7, 2015
1 parent a959148 commit 24ddd20
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Showing 2 changed files with 31 additions and 3 deletions.
23 changes: 23 additions & 0 deletions LICENSE.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
The MIT License

Copyright (c) 2015 Broad Institute

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
11 changes: 8 additions & 3 deletions main.c
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
#include "sdict.h"
#include "miniasm.h"

#define MA_VERSION "r31"
#define MA_VERSION "r41"

static void print_subs(const sdict_t *d, const ma_sub_t *sub)
{
Expand Down Expand Up @@ -41,7 +41,7 @@ int main(int argc, char *argv[])
char *fn_reads = 0, *outfmt = "ug";

ma_opt_init(&opt);
while ((c = getopt(argc, argv, "m:s:c:S:i:d:g:o:h:I:r:f:e:p:12")) >= 0) {
while ((c = getopt(argc, argv, "m:s:c:S:i:d:g:o:h:I:r:f:e:p:12V")) >= 0) {
if (c == 'm') opt.min_match = atoi(optarg);
else if (c == 'i') opt.min_iden = atof(optarg);
else if (c == 's') opt.min_span = atoi(optarg);
Expand All @@ -58,6 +58,10 @@ int main(int argc, char *argv[])
else if (c == 'p') outfmt = optarg;
else if (c == '1') no_first = 1;
else if (c == '2') no_second = 1;
else if (c == 'V') {
printf("%s\n", MA_VERSION);
return 0;
}
}
if (argc == optind) {
fprintf(stderr, "Usage: miniasm [options] <in.paf>\n");
Expand All @@ -77,10 +81,11 @@ int main(int argc, char *argv[])
fprintf(stderr, " -r FLOAT overlap drop ratio [%.2f]\n", opt.ovlp_drop_ratio);
fprintf(stderr, " -e INT small unitig threshold [%d]\n", opt.max_ext);
fprintf(stderr, " -f FILE read sequences []\n");
fprintf(stderr, " Steps:\n");
fprintf(stderr, " Miscellaneous:\n");
fprintf(stderr, " -p STR output information: bed, paf, sg or ug [%s]\n", outfmt);
fprintf(stderr, " -1 skip 1-pass read selection\n");
fprintf(stderr, " -2 skip 2-pass read selection\n");
fprintf(stderr, " -V print version number\n");
return 1;
}

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