1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
enum LoaderModes {
mode_Archive,
mode_Remap
};
typedef struct globals
{
char const *inpath;
char const *outpath;
char const *outname;
char const *firstOut;
char const *tmpfs;
struct KFile *noMatchLog;
char const *schemaPath;
char const *schemaIncludePath;
char const *refXRefPath;
char const *QualQuantizer;
char const *refFilter;
char const** refFiles; /* NULL-terminated array pointing to argv */
char const *headerText;
uint64_t maxAlignCount;
size_t cache_size;
unsigned errCount;
unsigned maxErrCount;
unsigned maxWarnCount_NoMatch;
unsigned maxWarnCount_DupConflict;
unsigned pid;
unsigned minMatchCount; /* minimum number of matches to count as an alignment */
int minMapQual;
enum LoaderModes mode;
enum LoaderModes globalMode;
uint32_t maxSeqLen;
bool omit_aligned_reads;
bool omit_reference_reads;
bool no_real_output;
bool expectUnsorted;
bool requireSorted;
bool noVerifyReferences;
bool onlyVerifyReferences;
bool useQUAL;
bool limit2config;
bool editAlignedQual;
bool keepMismatchQual;
bool acceptBadDups; /* accept spots with inconsistent PCR duplicate flags */
bool acceptNoMatch; /* accept without any matching bases */
bool noSpotAssembly;
uint8_t alignedQualValue;
bool allUnaligned; /* treat all records as unaligned */
bool noColorSpace;
bool noSecondary;
bool hasTI;
bool acceptHardClip;
bool allowMultiMapping; /* allow multiple reference names to map to the same real reference */
bool assembleWithSecondary;
bool deferSecondary;
} Globals;
extern Globals G;
|
