Mercurial > repos > aaronquinlan > multi_intersect
diff BEDTools-Version-2.14.3/src/bedToIgv/bedToIgv.cpp @ 1:bec36315bd12 default tip
Deleted selected files
author | aaronquinlan |
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date | Sat, 19 Nov 2011 14:17:03 -0500 |
parents | dfcd8b6c1bda |
children |
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--- a/BEDTools-Version-2.14.3/src/bedToIgv/bedToIgv.cpp Thu Nov 03 10:25:04 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,269 +0,0 @@ -/***************************************************************************** - bedToIgv.cpp - - (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. -******************************************************************************/ -#include "lineFileUtilities.h" -#include "bedFile.h" -#include "genomeFile.h" -#include "version.h" - -#include <vector> -#include <iostream> -#include <fstream> -#include <stdlib.h> - -using namespace std; - -// define our program name -#define PROGRAM_NAME "bedToIgv" - -// define our parameter checking macro -#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) - -// function declarations -void ShowHelp(void); - -void DetermineBedInput(BedFile *bed, string path, string sortType, string session, - bool collapse, bool useNames, string imageType, int slop); -void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session, - bool collapse, bool useNames, string imageType, int slop); - - -int main(int argc, char* argv[]) { - - // our configuration variables - bool showHelp = false; - - // input files - string bedFile = "stdin"; - string imagePath = "./"; - string sortType = "none"; - string session = "none"; - int slop = 0; - string imageType = "png"; - - bool haveBed = true; - bool collapse = false; - bool useNames = false; - - for(int i = 1; i < argc; i++) { - int parameterLength = (int)strlen(argv[i]); - - if((PARAMETER_CHECK("-h", 2, parameterLength)) || - (PARAMETER_CHECK("--help", 5, parameterLength))) { - showHelp = true; - } - } - - if(showHelp) ShowHelp(); - - // do some parsing (all of these parameters require 2 strings) - for(int i = 1; i < argc; i++) { - - int parameterLength = (int)strlen(argv[i]); - - if(PARAMETER_CHECK("-i", 2, parameterLength)) { - if ((i+1) < argc) { - bedFile = argv[i + 1]; - i++; - } - } - else if(PARAMETER_CHECK("-path", 5, parameterLength)) { - if ((i+1) < argc) { - imagePath = argv[i + 1]; - i++; - } - } - else if(PARAMETER_CHECK("-sort", 5, parameterLength)) { - if ((i+1) < argc) { - sortType = argv[i + 1]; - i++; - } - } - else if(PARAMETER_CHECK("-sess", 5, parameterLength)) { - if ((i+1) < argc) { - session = argv[i + 1]; - i++; - } - } - else if(PARAMETER_CHECK("-clps", 5, parameterLength)) { - collapse = true; - } - else if(PARAMETER_CHECK("-name", 5, parameterLength)) { - useNames = true; - } - else if(PARAMETER_CHECK("-slop", 5, parameterLength)) { - if ((i+1) < argc) { - slop = atoi(argv[i + 1]); - i++; - } - } - else if(PARAMETER_CHECK("-img", 4, parameterLength)) { - if ((i+1) < argc) { - imageType = argv[i + 1]; - i++; - } - } - else { - cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; - showHelp = true; - } - } - - // make sure we have an input files - if (!haveBed ) { - cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl; - showHelp = true; - } - if (sortType != "none") { - if ((sortType != "base") && (sortType != "position") && (sortType != "strand") && - (sortType != "quality") && (sortType != "sample") && (sortType != "readGroup")) { - cerr << endl << "*****" << endl << "*****ERROR: Invalid sort option. " << endl << "*****" << endl; - showHelp = true; - } - } - if (slop < 0) { - cerr << endl << "*****" << endl << "*****ERROR: Slop must be >= 0. " << endl << "*****" << endl; - showHelp = true; - } - - if (!showHelp) { - BedFile *bed = new BedFile(bedFile); - DetermineBedInput(bed, imagePath, sortType, session, collapse, useNames, imageType, slop); - } - else { - ShowHelp(); - } -} - - -void ShowHelp(void) { - - cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl; - - cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl; - - cerr << "Summary: Creates a batch script to create IGV images " << endl; - cerr << " at each interval defined in a BED/GFF/VCF file." << endl << endl; - - cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl; - - cerr << "Options: " << endl; - - cerr << "\t-path\t" << "The full path to which the IGV snapshots should be written." << endl; - cerr << "\t\t(STRING) Default: ./" << endl << endl; - - cerr << "\t-sess\t" << "The full path to an existing IGV session file to be " << endl; - cerr << "\t\tloaded prior to taking snapshots." << endl << endl; - cerr << "\t\t(STRING) Default is for no session to be loaded." << endl << endl; - - cerr << "\t-sort\t" << "The type of BAM sorting you would like to apply to each image. " << endl; - cerr << "\t\tOptions: base, position, strand, quality, sample, and readGroup" << endl; - cerr << "\t\tDefault is to apply no sorting at all." << endl << endl; - - cerr << "\t-clps\t" << "Collapse the aligned reads prior to taking a snapshot. " << endl; - cerr << "\t\tDefault is to no collapse." << endl << endl; - - cerr << "\t-name\t" << "Use the \"name\" field (column 4) for each image's filename. " << endl; - cerr << "\t\tDefault is to use the \"chr:start-pos.ext\"." << endl << endl; - - cerr << "\t-slop\t" << "Number of flanking base pairs on the left & right of the image." << endl; - cerr << "\t\t- (INT) Default = 0." << endl << endl; - - cerr << "\t-img\t" << "The type of image to be created. " << endl; - cerr << "\t\tOptions: png, eps, svg" << endl; - cerr << "\t\tDefault is png." << endl << endl; - - cerr << "Notes: " << endl; - cerr << "\t(1) The resulting script is meant to be run from within the IGV GUI version 1.5 or later." << endl; - cerr << "\t(2) Unless you use the -sess option, it is assumed that prior to running the script, " << endl; - cerr << "\t\tyou have loaded the proper genome, tracks and data files." << endl << endl; - - - // end the program here - exit(1); -} - - -void DetermineBedInput(BedFile *bed, string path, string sortType, string session, - bool collapse, bool useNames, string imageType, int slop) { - - // dealing with a proper file - if (bed->bedFile != "stdin") { - - ifstream bedStream(bed->bedFile.c_str(), ios::in); - if ( !bedStream ) { - cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl; - exit (1); - } - ProcessBed(bedStream, bed, path, sortType, session, collapse, useNames, imageType, slop); - } - // reading from stdin - else { - ProcessBed(cin, bed, path, sortType, session, collapse, useNames, imageType, slop); - } -} - - -void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session, - bool collapse, bool useNames, string imageType, int slop) { - - // set the image path - cout << "snapshotDirectory " << path << endl; - - // should we load a session - if (session != "none") - cout << "load " << session << endl; - - - BED bedEntry, nullBed; - int lineNum = 0; - BedLineStatus bedStatus; - - bed->Open(); - // process each BED entry and convert to an IGV request - while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) { - if (bedStatus == BED_VALID) { - - string filename = bedEntry.chrom + "_" + ToString(bedEntry.start) + "_" + ToString(bedEntry.end); - string locus = bedEntry.chrom + ":" + ToString(bedEntry.start - slop) + "-" + ToString(bedEntry.end + slop); - - if (useNames == true) { - if (bedEntry.name.empty() == false) - filename = filename + "_" + bedEntry.name; - else { - cerr << "Error: You requested that filenames be based upon the name field. However, it appears to be empty. Exiting!" << endl; - exit (1); - } - } - if (slop > 0) { - filename = filename + "_" + "slop" + ToString(slop); - } - // goto - cout << "goto " << locus << endl; - - // sort - if (sortType != "none") - cout << "sort " << sortType << endl; - - // collapse - if (collapse == true) - cout << "collapse" << endl; - - // snapshot - cout << "snapshot " << filename << "." << imageType << endl; - - // reset - bedEntry = nullBed; - } - } - // close up - bed->Close(); -}