/
fastagap.c
94 lines (81 loc) · 2.11 KB
/
fastagap.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
/*
* Copyright (C) 2011, Greg Benison
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
#include <getopt.h>
#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
int verbose_mode = 0;
int sequence_idx = 0;
int exon_start = 0;
int exon_mode = 0;
int idx = 0;
int first_exon_idx = 0;
static const int exon_min_length = 8;
const char *my_optstring = "v";
const struct option my_options[] = {
{"verbose", no_argument, NULL, 'v'},
{0,0,0,0}
};
static void
report_exon(int idx)
{
exon_mode = 0;
if ((idx - exon_start + 1) >= exon_min_length)
printf(" %d -- %d\n", exon_start, idx);
}
static void
start_exon()
{
exon_mode = 1;
exon_start = idx;
}
void process_option(int code, char *optarg) {
if (code == 'v') verbose_mode = 1;
}
void post_process() {}
void init_sequence() { exon_mode = 0; idx = 0; sequence_idx++; }
void
handle_sequence(char c)
{
++idx;
if (verbose_mode)
{
if ((c == '-') && exon_mode)
report_exon(idx - 1);
else if (!exon_mode && (c != '-')) start_exon();
}
else
{
if ((c != '-') && (first_exon_idx == 0))
first_exon_idx = idx;
}
}
void
terminate_sequence()
{
if (verbose_mode)
{
if (exon_mode) report_exon(idx);
}
else if (sequence_idx == 1)
printf ("%d", first_exon_idx);
}
void init_comment() { if (verbose_mode) printf("> "); }
void handle_comment(char c) { if (verbose_mode) putchar(c); }
void terminate_comment() { if (verbose_mode) putchar('\n'); }