Mercurial > repos > aaronquinlan > multi_intersect

comparison BEDTools-Version-2.14.3/src/coverageBed/coverageMain.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 coverageMain.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 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "coverageBed.h"
13 #include "version.h"
14
15 using namespace std;
16
17 // define the version
18 #define PROGRAM_NAME "coverageBed"
19
20 // define our parameter checking macro
21 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
22
23 // function declarations
24 void ShowHelp(void);
25
26 int main(int argc, char* argv[]) {
27
28 // our configuration variables
29 bool showHelp = false;
30
31 // input files
32 string bedAFile;
33 string bedBFile;
34
35 // parm flags
36 bool sameStrand = false;
37 bool diffStrand = false;
38 bool writeHistogram = false;
39 bool eachBase = false;
40 bool obeySplits = false;
41 bool bamInput = false;
42 bool haveBedA = false;
43 bool haveBedB = false;
44 bool countsOnly = false;
45
46 // check to see if we should print out some help
47 if(argc <= 1) showHelp = true;
48
49 for(int i = 1; i < argc; i++) {
50 int parameterLength = (int)strlen(argv[i]);
51
52 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
53 (PARAMETER_CHECK("--help", 5, parameterLength))) {
54 showHelp = true;
55 }
56 }
57
58 if(showHelp) ShowHelp();
59
60 // do some parsing (all of these parameters require 2 strings)
61 for(int i = 1; i < argc; i++) {
62
63 int parameterLength = (int)strlen(argv[i]);
64
65 if(PARAMETER_CHECK("-a", 2, parameterLength)) {
66 if ((i+1) < argc) {
67 haveBedA = true;
68 bedAFile = argv[i + 1];
69 i++;
70 }
71 }
72 else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
73 if ((i+1) < argc) {
74 haveBedA = true;
75 bamInput = true;
76 bedAFile = argv[i + 1];
77 i++;
78 }
79 }
80 else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
81 if ((i+1) < argc) {
82 haveBedB = true;
83 bedBFile = argv[i + 1];
84 i++;
85 }
86 }
87 else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
88 sameStrand = true;
89 }
90 else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
91 diffStrand = true;
92 }
93 else if (PARAMETER_CHECK("-hist", 5, parameterLength)) {
94 writeHistogram = true;
95 }
96 else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
97 eachBase = true;
98 }
99 else if (PARAMETER_CHECK("-split", 6, parameterLength)) {
100 obeySplits = true;
101 }
102 else if (PARAMETER_CHECK("-counts", 7, parameterLength)) {
103 countsOnly = true;
104 }
105 else {
106 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
107 showHelp = true;
108 }
109 }
110
111 // make sure we have both input files
112 if (!haveBedA || !haveBedB) {
113 cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
114 showHelp = true;
115 }
116
117 if (sameStrand && diffStrand) {
118 cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
119 showHelp = true;
120 }
121
122 if (!showHelp) {
123 BedCoverage *bg = new BedCoverage(bedAFile, bedBFile, sameStrand, diffStrand,
124 writeHistogram, bamInput, obeySplits, eachBase, countsOnly);
125 delete bg;
126 return 0;
127 }
128 else {
129 ShowHelp();
130 }
131 }
132
133 void ShowHelp(void) {
134
135 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
136
137 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
138
139 cerr << "Summary: Returns the depth and breadth of coverage of features from A" << endl;
140 cerr << "\t on the intervals in B." << endl << endl;
141
142 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
143
144 cerr << "Options: " << endl;
145
146 cerr << "\t-abam\t" << "The A input file is in BAM format." << endl << endl;
147
148 cerr << "\t-s\t" << "Require same strandedness. That is, only counts hits in A that" << endl;
149 cerr << "\t\toverlap B on the _same_ strand." << endl;
150 cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
151
152 cerr << "\t-S\t" << "Require different strandedness. That is, only report hits in A that" << endl;
153 cerr << "\t\toverlap B on the _opposite_ strand." << endl;
154 cerr << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
155
156 cerr << "\t-hist\t" << "Report a histogram of coverage for each feature in B" << endl;
157 cerr << "\t\tas well as a summary histogram for _all_ features in B." << endl << endl;
158 cerr << "\t\tOutput (tab delimited) after each feature in B:" << endl;
159 cerr << "\t\t 1) depth\n\t\t 2) # bases at depth\n\t\t 3) size of B\n\t\t 4) % of B at depth" << endl << endl;
160
161 cerr << "\t-d\t" << "Report the depth at each position in each B feature." << endl;
162 cerr << "\t\tPositions reported are one based. Each position" << endl;
163 cerr << "\t\tand depth follow the complete B feature." << endl << endl;
164
165 cerr << "\t-counts\t" << "Only report the count of overlaps, don't compute fraction, etc." << endl << endl;
166
167 cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl;
168 cerr << "\t\twhen computing coverage." << endl;
169 cerr << "\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations " << endl;
170 cerr << "\t\tto infer the blocks for computing coverage." << endl;
171 cerr << "\t\tFor BED12 files, this uses the BlockCount, BlockStarts," << endl;
172 cerr << "\t\tand BlockEnds fields (i.e., columns 10,11,12)." << endl << endl;
173
174 cerr << "Default Output: " << endl;
175 cerr << "\t" << " After each entry in B, reports: " << endl;
176 cerr << "\t 1) The number of features in A that overlapped the B interval." << endl;
177 cerr << "\t 2) The number of bases in B that had non-zero coverage." << endl;
178 cerr << "\t 3) The length of the entry in B." << endl;
179 cerr << "\t 4) The fraction of bases in B that had non-zero coverage." << endl << endl;
180
181 exit(1);
182 }