Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/progs/extract_qual.c @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
---|---|
date | Tue, 07 Jun 2011 17:48:05 -0400 |
parents | |
children |
rev | line source |
---|---|
0
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
1 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
2 * Copyright (c) Medical Research Council 1994-1999. All rights reserved. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
3 * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
4 * Permission to use, copy, modify and distribute this software and its |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
5 * documentation for any purpose is hereby granted without fee, provided that |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
6 * this copyright and notice appears in all copies. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
7 * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
8 * This file was written by James Bonfield, Simon Dear, Rodger Staden, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
9 * as part of the Staden Package at the MRC Laboratory of Molecular |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
10 * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
11 * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
12 * MRC disclaims all warranties with regard to this software. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
13 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
14 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
15 #include <stdio.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
16 #include <errno.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
17 #include <string.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
18 #include <strings.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
19 #include <stdlib.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
20 #include <unistd.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
21 #include <io_lib/Read.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
22 #include <io_lib/traceType.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
23 #include <io_lib/expFileIO.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
24 #include <io_lib/open_trace_file.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
25 #include <io_lib/xalloc.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
26 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
27 /* #include "stdio_hack.h" */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
28 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
29 #define LINE_LENGTH 60 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
30 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
31 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
32 * Converts the confidence array to the accuracy value string (AV). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
33 * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
34 * Note no memory overrun checks are performed on buf. It is recommended |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
35 * that it is allocated to 4*len (worst case of "100 " for each base). |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
36 * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
37 * Returns the buf argument. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
38 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
39 static char *my_conf2str(int1 *conf, int len, char *buf) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
40 int i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
41 char *ret = buf, *rs = buf; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
42 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
43 for (i = 0; i < len; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
44 sprintf(buf, "%d ", conf[i]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
45 buf += strlen(buf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
46 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
47 if (buf - rs > LINE_LENGTH) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
48 *buf++ = '\n'; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
49 *buf = '\0'; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
50 rs = buf; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
51 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
52 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
53 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
54 return ret; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
55 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
56 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
57 static int do_trans(mFILE *infp, char *in_file, FILE *outfp, int format, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
58 int good_only, int clip_cosmid, int fasta_out) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
59 Read *r; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
60 char *tmp_prob_A, *tmp_prob_C, *tmp_prob_G, *tmp_prob_T; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
61 char *cstr = NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
62 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
63 read_sections(READ_BASES); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
64 if (NULL == (r = mfread_reading(infp, in_file, format))) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
65 fprintf(stderr, "Failed to read file '%s'\n", in_file); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
66 return 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
67 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
68 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
69 tmp_prob_A = r->prob_A; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
70 tmp_prob_C = r->prob_C; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
71 tmp_prob_G = r->prob_G; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
72 tmp_prob_T = r->prob_T; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
73 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
74 #ifdef IOLIB_EXP |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
75 if (good_only && r->orig_trace_format == TT_EXP) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
76 int left=0, right=r->NBases + 1, val, lval, rval; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
77 Exp_info *e = (Exp_info *)r->orig_trace; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
78 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
79 if (0 == exp_get_int(e, EFLT_SL, &val)) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
80 if (val > left) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
81 left = val; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
82 if (0 == exp_get_int(e, EFLT_QL, &val)) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
83 if (val > left) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
84 left = val; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
85 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
86 if (0 == exp_get_int(e, EFLT_SR, &val)) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
87 if (val < right) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
88 right = val; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
89 if (0 == exp_get_int(e, EFLT_QR, &val)) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
90 if (val < right) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
91 right = val; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
92 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
93 /* This is horrid - see gap seqInfo.c file for explaination */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
94 if (clip_cosmid) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
95 int got_cosmid; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
96 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
97 if (0 == exp_get_rng(e, EFLT_CS, &lval, &rval)) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
98 got_cosmid = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
99 } else if (0 == exp_get_int(e, EFLT_CL, &lval) && |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
100 0 == exp_get_int(e, EFLT_CR, &rval)) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
101 got_cosmid = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
102 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
103 got_cosmid = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
104 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
105 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
106 if (got_cosmid) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
107 if (lval <= left && rval <= left) ; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
108 else if (lval <= left+1 && rval < right) left = rval; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
109 else if (lval <= left+1 && rval >= right) right = left+1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
110 else if (lval < right && rval < right) right = lval; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
111 else if (lval < right && rval >= right) right = lval; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
112 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
113 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
114 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
115 r->prob_A += left; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
116 r->prob_C += left; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
117 r->prob_G += left; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
118 r->prob_T += left; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
119 r->NBases = right - left - 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
120 } else |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
121 #endif /* IOLIB_EXP */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
122 if (good_only) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
123 r->prob_A += r->leftCutoff; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
124 r->prob_C += r->leftCutoff; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
125 r->prob_G += r->leftCutoff; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
126 r->prob_T += r->leftCutoff; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
127 r->NBases = r->rightCutoff - r->leftCutoff - 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
128 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
129 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
130 /* Confidence values */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
131 if (r->prob_A && r->prob_C && r->prob_G && r->prob_T && |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
132 r->NBases > 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
133 int i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
134 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
135 /* We have some, but are they non zero values? */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
136 for (i = 0; i < r->NBases; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
137 if (r->prob_A[i] || r->prob_C[i] || |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
138 r->prob_G[i] || r->prob_T[i]) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
139 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
140 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
141 if (i != r->NBases) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
142 int1 *conf = (int1 *)xmalloc(r->NBases); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
143 cstr = (char *)xmalloc(r->NBases * 4 + 2); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
144 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
145 for (i = 0; i < r->NBases; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
146 switch (r->base[i]) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
147 case 'a': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
148 case 'A': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
149 conf[i] = r->prob_A[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
150 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
151 case 'c': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
152 case 'C': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
153 conf[i] = r->prob_C[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
154 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
155 case 'g': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
156 case 'G': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
157 conf[i] = r->prob_G[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
158 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
159 case 't': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
160 case 'T': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
161 conf[i] = r->prob_T[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
162 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
163 case 'b': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
164 case 'B': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
165 conf[i] = (r->prob_C[i] + r->prob_G[i] + r->prob_T[i]) / 3; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
166 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
167 case 'd': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
168 case 'D': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
169 conf[i] = (r->prob_A[i] + r->prob_G[i] + r->prob_T[i]) / 3; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
170 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
171 case 'h': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
172 case 'H': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
173 conf[i] = (r->prob_A[i] + r->prob_C[i] + r->prob_T[i]) / 3; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
174 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
175 case 'v': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
176 case 'V': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
177 conf[i] = (r->prob_A[i] + r->prob_C[i] + r->prob_G[i]) / 3; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
178 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
179 case 'k': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
180 case 'K': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
181 conf[i] = (r->prob_G[i] + r->prob_T[i]) / 2; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
182 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
183 case 'm': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
184 case 'M': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
185 conf[i] = (r->prob_A[i] + r->prob_C[i]) / 2; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
186 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
187 case 'r': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
188 case 'R': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
189 conf[i] = (r->prob_A[i] + r->prob_G[i]) / 2; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
190 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
191 case 's': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
192 case 'S': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
193 conf[i] = (r->prob_C[i] + r->prob_G[i]) / 2; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
194 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
195 case 'w': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
196 case 'W': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
197 conf[i] = (r->prob_A[i] + r->prob_T[i]) / 2; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
198 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
199 case 'y': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
200 case 'Y': |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
201 conf[i] = (r->prob_C[i] + r->prob_T[i]) / 2; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
202 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
203 default: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
204 conf[i] = (r->prob_A[i] + r->prob_C[i] + r->prob_G[i] + r->prob_T[i]) / 4; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
205 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
206 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
207 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
208 my_conf2str(conf, r->NBases, cstr); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
209 xfree(conf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
210 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
211 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
212 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
213 if (fasta_out) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
214 char *p = strrchr(in_file, '/'); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
215 /* Add header */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
216 if (NULL == p) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
217 p = in_file; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
218 else |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
219 p++; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
220 fprintf(outfp, ">%s\n", p); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
221 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
222 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
223 if (cstr) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
224 fprintf(outfp,"%s\n", cstr); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
225 xfree(cstr); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
226 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
227 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
228 r->prob_A = tmp_prob_A; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
229 r->prob_C = tmp_prob_C; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
230 r->prob_G = tmp_prob_G; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
231 r->prob_T = tmp_prob_T; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
232 read_deallocate(r); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
233 fflush(outfp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
234 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
235 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
236 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
237 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
238 static void usage(void) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
239 fprintf(stderr, "Usage: extract_qual [-r] [-(abi|alf|scf|exp|pln|ctf|ztr)]\n" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
240 " [-good_only] [-clip_cosmid] [-fasta_out]\n" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
241 " [-output output_name] [input_name] ...\n"); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
242 exit(1); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
243 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
244 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
245 int main(int argc, char **argv) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
246 int from_stdin = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
247 mFILE *infp = mstdin(); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
248 FILE *outfp = stdout; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
249 int format = TT_ANY; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
250 int redirect = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
251 int good_only = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
252 int clip_cosmid = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
253 int fasta_out = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
254 int ret = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
255 char *fofn = NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
256 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
257 for (argc--, argv++; argc > 0; argc--, argv++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
258 if (strcmp(*argv, "-r") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
259 redirect = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
260 } else if (strcasecmp(*argv, "-abi") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
261 format = TT_ABI; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
262 } else if (strcasecmp(*argv, "-alf") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
263 format = TT_ALF; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
264 } else if (strcasecmp(*argv, "-scf") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
265 format = TT_SCF; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
266 } else if (strcasecmp(*argv, "-exp") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
267 format = TT_EXP; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
268 } else if (strcasecmp(*argv, "-pln") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
269 format = TT_PLN; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
270 } else if (strcasecmp(*argv, "-ztr") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
271 format = TT_ZTR; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
272 } else if (strcasecmp(*argv, "-ctf") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
273 format = TT_CTF; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
274 } else if (strcasecmp(*argv, "-good_only") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
275 good_only = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
276 } else if (strcasecmp(*argv, "-clip_cosmid") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
277 clip_cosmid = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
278 } else if (strcasecmp(*argv, "-fasta_out") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
279 fasta_out = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
280 } else if (strcmp(*argv, "-fofn") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
281 fofn = *++argv; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
282 argc--; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
283 from_stdin = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
284 } else if (strcasecmp(*argv, "-output") == 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
285 if (NULL == (outfp = fopen(*++argv, "wb"))) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
286 perror(*argv); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
287 return 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
288 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
289 argc--; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
290 } else if (**argv != '-') { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
291 from_stdin = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
292 break; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
293 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
294 usage(); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
295 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
296 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
297 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
298 read_experiment_redirect(redirect); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
299 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
300 if (!from_stdin) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
301 if (fofn) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
302 FILE *fofn_fp; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
303 char line[8192]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
304 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
305 if (strcmp(fofn, "stdin") == 0) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
306 fofn_fp = stdin; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
307 else |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
308 fofn_fp = fopen(fofn, "r"); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
309 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
310 if (fofn_fp) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
311 while (fgets(line, 8192, fofn_fp) != NULL) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
312 char *cp; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
313 if (cp = strchr(line, '\n')) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
314 *cp = 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
315 if (format == TT_EXP) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
316 infp = open_exp_mfile(line, NULL); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
317 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
318 infp = open_trace_mfile(line, NULL); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
319 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
320 if (NULL == infp) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
321 perror(line); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
322 ret = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
323 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
324 ret |= do_trans(infp, line, outfp, format, good_only, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
325 clip_cosmid, fasta_out); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
326 mfclose(infp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
327 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
328 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
329 fclose(fofn_fp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
330 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
331 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
332 for (;argc > 0; argc--, argv++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
333 if (format == TT_EXP) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
334 infp = open_exp_mfile(*argv, NULL); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
335 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
336 infp = open_trace_mfile(*argv, NULL); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
337 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
338 if (NULL == infp) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
339 perror(*argv); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
340 ret = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
341 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
342 ret |= do_trans(infp, *argv, outfp, format, good_only, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
343 clip_cosmid, fasta_out); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
344 mfclose(infp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
345 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
346 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
347 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
348 ret = do_trans(infp, "<stdin>", outfp, format, good_only, clip_cosmid, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
349 fasta_out); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
350 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
351 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
352 return ret; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
353 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
354 |