|
0
|
1 /*****************************************************************************
|
|
|
2 tabFile.cpp
|
|
|
3
|
|
|
4 (c) 2009 - Aaron Quinlan
|
|
|
5 Hall Laboratory
|
|
|
6 Department of Biochemistry and Molecular Genetics
|
|
|
7 University of Virginia
|
|
|
8 aaronquinlan@gmail.com
|
|
|
9
|
|
|
10 Licensed under the GNU General Public License 2.0 license.
|
|
|
11 ******************************************************************************/
|
|
|
12 #include "lineFileUtilities.h"
|
|
|
13 #include "tabFile.h"
|
|
|
14
|
|
|
15 /*******************************************
|
|
|
16 Class methods
|
|
|
17 *******************************************/
|
|
|
18
|
|
|
19 // Constructor
|
|
|
20 TabFile::TabFile(const string &tabFile)
|
|
|
21 : _tabFile(tabFile)
|
|
|
22 {}
|
|
|
23
|
|
|
24 // Destructor
|
|
|
25 TabFile::~TabFile(void) {
|
|
|
26 }
|
|
|
27
|
|
|
28
|
|
|
29 void TabFile::Open(void) {
|
|
|
30 if (_tabFile == "stdin") {
|
|
|
31 _tabStream = &cin;
|
|
|
32 }
|
|
|
33 else {
|
|
|
34 size_t foundPos;
|
|
|
35 foundPos = _tabFile.find_last_of(".gz");
|
|
|
36 // is this a GZIPPED TAB file?
|
|
|
37 if (foundPos == _tabFile.size() - 1) {
|
|
|
38 igzstream tabs(_tabFile.c_str(), ios::in);
|
|
|
39 if ( !tabs ) {
|
|
|
40 cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl;
|
|
|
41 exit (1);
|
|
|
42 }
|
|
|
43 else {
|
|
|
44 // if so, close it (this was just a test)
|
|
|
45 tabs.close();
|
|
|
46 // now set a pointer to the stream so that we
|
|
|
47 // can read the file later on.
|
|
|
48 _tabStream = new igzstream(_tabFile.c_str(), ios::in);
|
|
|
49 }
|
|
|
50 }
|
|
|
51 // not GZIPPED.
|
|
|
52 else {
|
|
|
53
|
|
|
54 ifstream tabs(_tabFile.c_str(), ios::in);
|
|
|
55 // can we open the file?
|
|
|
56 if ( !tabs ) {
|
|
|
57 cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl;
|
|
|
58 exit (1);
|
|
|
59 }
|
|
|
60 else {
|
|
|
61 // if so, close it (this was just a test)
|
|
|
62 tabs.close();
|
|
|
63 // now set a pointer to the stream so that we
|
|
|
64 // can read the file later on.
|
|
|
65 _tabStream = new ifstream(_tabFile.c_str(), ios::in);
|
|
|
66 }
|
|
|
67 }
|
|
|
68 }
|
|
|
69 }
|
|
|
70
|
|
|
71
|
|
|
72 // Close the TAB file
|
|
|
73 void TabFile::Close(void) {
|
|
|
74 if (_tabFile != "stdin") delete _tabStream;
|
|
|
75 }
|
|
|
76
|
|
|
77
|
|
|
78 TabLineStatus TabFile::GetNextTabLine(TAB_FIELDS &tabFields, int &lineNum) {
|
|
|
79
|
|
|
80 // make sure there are still lines to process.
|
|
|
81 // if so, tokenize, return the TAB_FIELDS.
|
|
|
82 if (_tabStream->good() == true) {
|
|
|
83 string tabLine;
|
|
|
84 tabFields.reserve(20);
|
|
|
85
|
|
|
86 // parse the tabStream pointer
|
|
|
87 getline(*_tabStream, tabLine);
|
|
|
88 lineNum++;
|
|
|
89
|
|
|
90 // split into a string vector.
|
|
|
91 Tokenize(tabLine, tabFields);
|
|
|
92
|
|
|
93 // parse the line and validate it
|
|
|
94 return parseTabLine(tabFields, lineNum);
|
|
|
95 }
|
|
|
96
|
|
|
97 // default if file is closed or EOF
|
|
|
98 return TAB_INVALID;
|
|
|
99 }
|
