Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/io_lib/read_scf.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. 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 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
16 Title: read_scf.c |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
17 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
18 Purpose: read IO of Standard Chromatogram Format sequences |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
19 Last update: August 18 1994 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
20 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
21 Change log: |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
22 4 Feb 1992, Now draft proposal version 2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
23 20 Feb 1992, Grab info from comment lines |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
24 19 Aug 1992, If SCF file has clip information, don't clip automatically |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
25 10 Nov 1992 SCF comments now stored in seq data structure |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
26 18 Aug 1994 Renamed from ReadIOSCF.c; now purely SCF IO (no Seq structs) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
27 |
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 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
30 /* ---- Imports ---- */ |
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 #include <ctype.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
33 #include <stdio.h> /* IMPORT: fopen, fclose, fseek, ftell, fgetc, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
34 EOF */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
35 #include <stdlib.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
36 #include <string.h> |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
37 #include <sys/types.h> |
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 #include "io_lib/mach-io.h" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
40 #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
|
41 #include "io_lib/compress.h" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
42 #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
|
43 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
44 #include "io_lib/stdio_hack.h" |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
45 #include "io_lib/scf.h" /* SCF structures */ |
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 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
48 /* SunOS4 has it's definitions in unistd, which we won't include for compat. */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
49 #ifndef SEEK_SET |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
50 #define SEEK_SET 0 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
51 #define SEEK_CUR 1 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
52 #define SEEK_END 2 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
53 #endif |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
54 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
55 /* ---- Exported functions ---- */ |
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 int read_scf_header(FILE *fp, Header *h) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
58 { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
59 int i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
60 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
61 if (be_read_int_4(fp,&h->magic_number)==False) return -1; |
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 if (h->magic_number != SCF_MAGIC) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
64 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
65 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
66 if (be_read_int_4(fp,&h->samples)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
67 if (be_read_int_4(fp,&h->samples_offset)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
68 if (be_read_int_4(fp,&h->bases)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
69 if (be_read_int_4(fp,&h->bases_left_clip)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
70 if (be_read_int_4(fp,&h->bases_right_clip)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
71 if (be_read_int_4(fp,&h->bases_offset)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
72 if (be_read_int_4(fp,&h->comments_size)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
73 if (be_read_int_4(fp,&h->comments_offset)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
74 if (fread(&h->version[0],sizeof(h->version),1,fp)!=1) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
75 if (be_read_int_4(fp,&h->sample_size)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
76 if (be_read_int_4(fp,&h->code_set)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
77 if (be_read_int_4(fp,&h->private_size)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
78 if (be_read_int_4(fp,&h->private_offset)==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
79 for (i=0;i<18;i++) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
80 if (be_read_int_4(fp,&h->spare[i])==False) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
81 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
82 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
83 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
84 |
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 int read_scf_sample1(FILE *fp, Samples1 *s) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
87 { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
88 uint_1 buf[4]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
89 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
90 if (4 != fread(buf, 1, 4, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
91 s->sample_A = buf[0]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
92 s->sample_C = buf[1]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
93 s->sample_G = buf[2]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
94 s->sample_T = buf[3]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
95 |
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 (1 != fread(s, 4, 1, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
98 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
99 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
100 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
101 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
102 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
103 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
104 int read_scf_sample2(FILE *fp, Samples2 *s) |
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 uint_2 buf[4]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
107 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
108 if (4 != fread(buf, 2, 4, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
109 s->sample_A = be_int2(buf[0]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
110 s->sample_C = be_int2(buf[1]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
111 s->sample_G = be_int2(buf[2]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
112 s->sample_T = be_int2(buf[3]); |
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 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
115 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
116 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
117 int read_scf_samples1(FILE *fp, Samples1 *s, size_t num_samples) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
118 size_t i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
119 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
120 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
121 if (-1 == read_scf_sample1(fp, &(s[i]))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
122 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
123 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
124 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
125 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
126 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
127 |
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 int read_scf_samples2(FILE *fp, Samples2 *s, size_t num_samples) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
130 size_t i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
131 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
132 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
133 if (-1 == read_scf_sample2(fp, &(s[i]))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
134 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
135 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
136 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
137 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
138 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
139 |
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 int read_scf_samples32(FILE *fp, Samples2 *s, size_t num_samples) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
142 size_t i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
143 uint2 *samples_out; |
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 /* version to read delta delta data in 2 bytes */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
146 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
147 if ( ! (samples_out = (uint2 *)xmalloc((num_samples+1) * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
148 sizeof(uint2)))) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
149 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
150 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
151 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
152 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
153 if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
154 #ifdef SP_LITTLE_ENDIAN |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
155 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
156 samples_out[i] = be_int2(samples_out[i]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
157 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
158 #endif |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
159 scf_delta_samples2 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
160 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
161 (&s[i])->sample_A = samples_out[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
162 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
163 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
164 if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
165 #ifdef SP_LITTLE_ENDIAN |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
166 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
167 samples_out[i] = be_int2(samples_out[i]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
168 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
169 #endif |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
170 scf_delta_samples2 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
171 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
172 (&s[i])->sample_C = samples_out[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
173 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
174 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
175 if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
176 #ifdef SP_LITTLE_ENDIAN |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
177 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
178 samples_out[i] = be_int2(samples_out[i]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
179 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
180 #endif |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
181 scf_delta_samples2 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
182 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
183 (&s[i])->sample_G = samples_out[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
184 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
185 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
186 if (num_samples != fread(samples_out, 2, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
187 #ifdef SP_LITTLE_ENDIAN |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
188 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
189 samples_out[i] = be_int2(samples_out[i]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
190 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
191 #endif |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
192 scf_delta_samples2 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
193 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
194 (&s[i])->sample_T = samples_out[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
195 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
196 xfree(samples_out); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
197 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
198 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
199 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
200 int read_scf_samples31(FILE *fp, Samples1 *s, size_t num_samples) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
201 size_t i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
202 int1 *samples_out; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
203 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
204 /* version to read delta delta data in 1 byte */ |
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 if ( ! (samples_out = (int1 *)xmalloc((num_samples+1) * |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
207 sizeof(int1)))) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
208 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
209 } |
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 if (num_samples != fread(samples_out, 1, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
212 scf_delta_samples1 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
213 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
214 (&s[i])->sample_A = samples_out[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
215 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
216 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
217 if (num_samples != fread(samples_out, 1, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
218 scf_delta_samples1 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
219 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
220 (&s[i])->sample_C = samples_out[i]; |
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 (num_samples != fread(samples_out, 1, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
224 scf_delta_samples1 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
225 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
226 (&s[i])->sample_G = samples_out[i]; |
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 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
229 if (num_samples != fread(samples_out, 1, num_samples, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
230 scf_delta_samples1 ( samples_out, num_samples, 0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
231 for (i = 0; i < num_samples; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
232 (&s[i])->sample_T = samples_out[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
233 } |
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 xfree(samples_out); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
236 return 0; |
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 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
239 int read_scf_base(FILE *fp, Bases *b) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
240 { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
241 uint_1 buf[12]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
242 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
243 if (1 != fread(buf, 12, 1, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
244 b->peak_index = be_int4(((uint_4 *)buf)[0]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
245 b->prob_A = buf[4]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
246 b->prob_C = buf[5]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
247 b->prob_G = buf[6]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
248 b->prob_T = buf[7]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
249 b->base = buf[8]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
250 b->spare[0] = buf[9]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
251 b->spare[1] = buf[10]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
252 b->spare[2] = buf[11]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
253 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
254 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
255 } |
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 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
258 int read_scf_bases(FILE *fp, Bases *b, size_t num_bases) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
259 size_t i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
260 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
261 for (i = 0; i < num_bases; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
262 if (-1 == read_scf_base(fp, &(b[i]))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
263 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
264 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
265 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
266 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
267 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
268 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
269 int read_scf_bases3(FILE *fp, Bases *b, size_t num_bases) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
270 { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
271 size_t i; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
272 uint_4 *buf4; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
273 uint_1 *buf1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
274 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
275 if (NULL == (buf4 = (uint_4 *)xmalloc(1 + 4 * num_bases))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
276 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
277 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
278 if (NULL == (buf1 = (uint_1 *)xmalloc(1 + 8 * num_bases))) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
279 xfree(buf4); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
280 return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
281 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
282 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
283 if (num_bases != fread(buf4, 4, num_bases, fp)) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
284 for (i=0; i < num_bases; i++) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
285 (&b[i])->peak_index = be_int4(buf4[i]); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
286 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
287 if (8 * num_bases != fread(buf1, 1, 8 * num_bases, fp)) 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 for (i=0; i < num_bases; i++) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
290 (&b[i])->prob_A = buf1[i]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
291 (&b[i])->prob_C = buf1[i+num_bases]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
292 (&b[i])->prob_G = buf1[i+2*num_bases]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
293 (&b[i])->prob_T = buf1[i+3*num_bases]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
294 (&b[i])->base = buf1[i+4*num_bases]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
295 (&b[i])->spare[0] = buf1[i+5*num_bases]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
296 (&b[i])->spare[1] = buf1[i+6*num_bases]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
297 (&b[i])->spare[2] = buf1[i+7*num_bases]; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
298 } |
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 xfree(buf4); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
301 xfree(buf1); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
302 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
303 return 0; |
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 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
306 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
307 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
308 int read_scf_comment(FILE *fp, Comments *c, size_t s) |
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 (fread(c, 1, s, fp) != s) return -1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
311 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
312 return 0; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
313 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
314 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
315 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
316 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
317 * Read the SCF format sequence from FILE *fp into a 'scf' structure. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
318 * A NULL result indicates failure. |
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 Scf *fread_scf(FILE *fp) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
321 Scf *scf; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
322 Header h; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
323 int err; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
324 float scf_version; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
325 int sections = read_sections(0); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
326 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
327 /* Read header */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
328 if (read_scf_header(fp, &h) == -1) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
329 return NULL; |
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 /* Allocate memory */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
333 if (NULL == (scf = scf_allocate(h.samples, h.sample_size, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
334 h.bases, h.comments_size, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
335 h.private_size))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
336 return 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 /* fake things for older style SCF -- SD */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
339 if (h.sample_size != 1 && h.sample_size != 2) h.sample_size = 1; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
340 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
341 scf_version = scf_version_str2float(h.version); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
342 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
343 memcpy(&scf->header, &h, sizeof(Header)); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
344 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
345 if (sections & READ_SAMPLES) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
346 /* Read samples */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
347 if (fseek(fp, (off_t)h.samples_offset, 0 /* SEEK_SET */) != 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
348 scf_deallocate(scf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
349 return NULL; |
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 if ( 2.9 > scf_version ) { |
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 if (h.sample_size == 1) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
355 err= read_scf_samples1(fp, scf->samples.samples1, h.samples); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
356 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
357 else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
358 err= read_scf_samples2(fp, scf->samples.samples2, h.samples); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
359 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
360 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
361 else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
362 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
363 if (h.sample_size == 1) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
364 err= read_scf_samples31(fp, scf->samples.samples1, h.samples); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
365 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
366 else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
367 err= read_scf_samples32(fp, scf->samples.samples2, h.samples); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
368 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
369 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
370 if (-1 == err) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
371 scf_deallocate(scf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
372 return NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
373 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
374 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
375 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
376 if (sections & READ_BASES) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
377 /* Read bases */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
378 if (fseek(fp, (off_t)h.bases_offset, 0 /* SEEK_SET */) != 0) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
379 scf_deallocate(scf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
380 return NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
381 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
382 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
383 if ( 2.9 > scf_version ) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
384 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
385 if (-1 == read_scf_bases(fp, scf->bases, h.bases)) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
386 scf_deallocate(scf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
387 return NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
388 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
389 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
390 else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
391 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
392 if (-1 == read_scf_bases3(fp, scf->bases, h.bases)) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
393 scf_deallocate(scf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
394 return NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
395 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
396 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
397 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
398 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
399 if (sections & READ_COMMENTS) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
400 /* Read comments */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
401 if (scf->comments) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
402 if (fseek(fp,(off_t)(h.comments_offset), 0) != 0 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
403 || -1 == read_scf_comment(fp, scf->comments, |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
404 h.comments_size)) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
405 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
406 * Was: "scf_deallocate(scf); return NULL;". |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
407 * We now simply clear the comments and gracefully continue. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
408 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
409 fprintf(stderr, "Warning: SCF file had invalid comment field\n"); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
410 xfree(scf->comments); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
411 scf->comments = NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
412 } else { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
413 scf->comments[h.comments_size] = '\0'; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
414 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
415 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
416 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
417 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
418 /* Read private data */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
419 if (h.private_size) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
420 if (-1 == fseek(fp, (off_t)(h.private_offset), 0) || |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
421 h.private_size != fread(scf->private_data, 1, h.private_size, fp)){ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
422 scf_deallocate(scf); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
423 return NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
424 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
425 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
426 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
427 return scf; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
428 } |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
429 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
430 /* |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
431 * Read the SCF format sequence with name `fn' into a 'scf' structure. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
432 * A NULL result indicates failure. |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
433 */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
434 Scf *read_scf(char *fn) { |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
435 Scf *scf; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
436 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
437 FILE *fp; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
438 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
439 /* Open fn for reading in binary mode */ |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
440 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
441 if (NULL == (fp = fopen_compressed(fn, NULL))) |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
442 return NULL; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
443 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
444 scf = fread_scf(fp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
445 fclose(fp); |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
446 |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
447 return scf; |
d901c9f41a6a
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
dawe
parents:
diff
changeset
|
448 } |