From ffa852df3aa4c54c41e06a33400f3b42f29deda7 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 23 Mar 2010 16:30:03 -0400
Subject: [PATCH] slopBed now uses the GenomeFile class.
---
src/slopBed/Makefile | 7 +++---
src/slopBed/slopBed.cpp | 51 ++++++++++-------------------------------
src/slopBed/slopBed.h | 18 ++++++++-------
3 files changed, 26 insertions(+), 50 deletions(-)
diff --git a/src/slopBed/Makefile b/src/slopBed/Makefile
index f5c1c618..fff5a637 100755
--- a/src/slopBed/Makefile
+++ b/src/slopBed/Makefile
@@ -9,14 +9,14 @@ BIN_DIR = ../../bin/
# -------------------
# define our includes
# -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/genomeFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= slopBedMain.cpp slopBed.cpp
OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o
+_EXT_OBJECTS=bedFile.o genomeFile.o lineFileUtilities.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
PROGRAM= slopBed
@@ -37,7 +37,8 @@ $(BUILT_OBJECTS): $(SOURCES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
-
+ @$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/genomeFile/
+
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
diff --git a/src/slopBed/slopBed.cpp b/src/slopBed/slopBed.cpp
index a5054d79..590bf2bc 100755
--- a/src/slopBed/slopBed.cpp
+++ b/src/slopBed/slopBed.cpp
@@ -12,9 +12,7 @@
#include "lineFileUtilities.h"
#include "slopBed.h"
-/*
- Constructor
-*/
+
BedSlop::BedSlop(string &bedFile, string &genomeFile, bool &forceStrand, int &leftSlop, int &rightSlop) {
this->bedFile = bedFile;
@@ -24,14 +22,11 @@ BedSlop::BedSlop(string &bedFile, string &genomeFile, bool &forceStrand, int &le
this->leftSlop = leftSlop;
this->rightSlop = rightSlop;
- this->bed = new BedFile(bedFile);
+ this->bed = new BedFile(bedFile);
+ this->genome = new GenomeFile(genomeFile);
}
-
-/*
- Destructor
-*/
BedSlop::~BedSlop(void) {
}
@@ -49,7 +44,6 @@ void BedSlop::SlopBed(istream &bedInput) {
lineNum++;
BED bedEntry; // used to store the current BED line from the BED file.
-
if (this->bed->parseLine(bedEntry, bedFields, lineNum)) {
AddSlop(bedEntry);
bed->reportBedNewLine(bedEntry);
@@ -60,18 +54,18 @@ void BedSlop::SlopBed(istream &bedInput) {
void BedSlop::AddSlop(BED &bed) {
- /*
- special handling if the BED entry is on the negative
- strand and the user cares about strandedness.
- */
- if ((this->forceStrand) && (bed.strand == "-")) {
+ // special handling if the BED entry is on the negative
+ // strand and the user cares about strandedness.
+ int chromSize = genome->getChromSize(bed.chrom);
+
+ if ( (this->forceStrand) && (bed.strand == "-") ) {
// inspect the start
if ((bed.start - rightSlop) > 0) bed.start -= rightSlop;
else bed.start = 0;
// inspect the start
- if ((bed.end + leftSlop) <= this->chromSizes[bed.chrom]) bed.end += leftSlop;
- else bed.end = this->chromSizes[bed.chrom];
+ if ((bed.end + leftSlop) <= chromSize) bed.end += leftSlop;
+ else bed.end = chromSize;
}
else {
// inspect the start
@@ -79,35 +73,14 @@ void BedSlop::AddSlop(BED &bed) {
else bed.start = 0;
// inspect the end
- if ((bed.end + rightSlop) <= this->chromSizes[bed.chrom]) bed.end += rightSlop;
- else bed.end = this->chromSizes[bed.chrom];
+ if ((bed.end + rightSlop) <= chromSize) bed.end += rightSlop;
+ else bed.end = chromSize;
}
}
void BedSlop::DetermineBedInput() {
-
- /* open the GENOME file for reading.
- if successful, load each chrom and it's size into
- the "chromSize" map. also compute the total size of the genome
- and store in "genomeSize"
- */
- ifstream genome(this->genomeFile.c_str(), ios::in);
- if ( !genome ) {
- cerr << "Error: The requested genome file (" <<this->genomeFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- else {
- string chrom;
- unsigned int size;
- while (genome >> chrom >> size) {
- if (chrom.size() > 0 && size > 0) {
- this->chromSizes[chrom] = size;
- }
- }
- }
-
if (this->bedFile != "stdin") { // process a file
ifstream beds(this->bedFile.c_str(), ios::in);
if ( !beds ) {
diff --git a/src/slopBed/slopBed.h b/src/slopBed/slopBed.h
index 272ca797..e6dbce0e 100755
--- a/src/slopBed/slopBed.h
+++ b/src/slopBed/slopBed.h
@@ -1,9 +1,3 @@
-#include "bedFile.h"
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <map>
-#include <cstdlib>
/*****************************************************************************
slopBed.h
@@ -15,6 +9,15 @@
Licenced under the GNU General Public License 2.0+ license.
******************************************************************************/
+
+#include "bedFile.h"
+#include "genomeFile.h"
+
+#include <vector>
+#include <iostream>
+#include <fstream>
+#include <map>
+#include <cstdlib>
#include <ctime>
using namespace std;
@@ -49,6 +52,5 @@ private:
int rightSlop;
BedFile *bed;
-
- map<string, int, less<string> > chromSizes;
+ GenomeFile *genome;
};
--
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