intersectHelp.cpp 1.59 KB
Newer Older
nkindlon's avatar
nkindlon committed
1
/*****************************************************************************
2
  intersectHelp.cpp
nkindlon's avatar
nkindlon committed
3
4
5
6
7
8
9
10
11
12

  (c) 2009 - Aaron Quinlan
  Hall Laboratory
  Department of Biochemistry and Molecular Genetics
  University of Virginia
  aaronquinlan@gmail.com

  Licenced under the GNU General Public License 2.0 license.
******************************************************************************/

nkindlon's avatar
nkindlon committed
13
#include "CommonHelp.h"
nkindlon's avatar
nkindlon committed
14
15
16
17
18
19
20

void intersect_help(void) {

    cerr << "\nTool:    bedtools intersect (aka intersectBed)" << endl;
    cerr << "Version: " << VERSION << "\n";    
    cerr << "Summary: Report overlaps between two feature files." << endl << endl;

21
    cerr << "Usage:   " << "bedtools intersect" << " [OPTIONS] -a <bed/gff/vcf/bam> -b <bed/gff/vcf/bam>" << endl << endl;
nkindlon's avatar
nkindlon committed
22

arq5x's avatar
arq5x committed
23
24
    cerr << "\t"				<< "Note: -b may be followed with multiple databases and/or " << endl;
    cerr << "\t"					"wildcard (*) character(s). " << endl;
nkindlon's avatar
nkindlon committed
25

nkindlon's avatar
nkindlon committed
26
27
    cerr << "Options: " << endl;

28
29
    // -abam is obsolete.
    // cerr << "\t-abam\t"         << "The A input file is in BAM format.  Output will be BAM as well." << endl << endl;
nkindlon's avatar
nkindlon committed
30
31


32
33
    IntersectOutputHelp();
    IntersectCommonHelp();
nkindlon's avatar
nkindlon committed
34

35
    sortedHelp();
36
    multiDbOutputHelp();
37
    allToolsCommonHelp();
nkindlon's avatar
nkindlon committed
38

nkindlon's avatar
nkindlon committed
39
40
41
42
43
44
45
46
47
    cerr << "Notes: " << endl;
    cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
    cerr << "\tand exlcuded if an overlap cannot be found.  If multiple overlaps exist, they are not" << endl;
    cerr << "\treported, as we are only testing for one or more overlaps." << endl << endl;

    // end the program here
    exit(1);

}