Added initial, untested version of pairToPair

0897e908 · Aaron · 7f9adc15 · 0897e908 · 0897e908 · 0897e908
Commit 0897e908 authored 15 years ago by Aaron
--- a/Makefile
+++ b/Makefile
@@ -19,7 +19,7 @@ export CXX ?= g++
 #include includes/$(BLD_PLATFORM).inc

 # define our source subdirectories
-SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/peIntersectBed
+SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/peIntersectBed $(SRC_DIR)/pairToPair $(SRC_DIR)/maskFastaFromBed

 UTIL_SUBDIRS =  $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities


--- a/bin/closestBed
+++ b/bin/closestBed
--- a/bin/complementBed
+++ b/bin/complementBed
--- a/bin/coverageBed
+++ b/bin/coverageBed
--- a/bin/fastaFromBed
+++ b/bin/fastaFromBed
--- a/bin/genomeCoverageBed
+++ b/bin/genomeCoverageBed
--- a/bin/linksBed
+++ b/bin/linksBed
--- a/bin/maskFastaFromBed
+++ b/bin/maskFastaFromBed
--- a/bin/mergeBed
+++ b/bin/mergeBed
--- a/bin/pairToPair
+++ b/bin/pairToPair
--- a/bin/peIntersectBed
+++ b/bin/peIntersectBed
--- a/bin/shuffleBed
+++ b/bin/shuffleBed
--- a/bin/slopBed
+++ b/bin/slopBed
--- a/bin/sortBed
+++ b/bin/sortBed
--- a/bin/subtractBed
+++ b/bin/subtractBed
--- a/bin/windowBed
+++ b/bin/windowBed
--- a/obj/bedFilePE.o
+++ b/obj/bedFilePE.o
--- a/obj/closestBed.o
+++ b/obj/closestBed.o
--- a/obj/closestMain.o
+++ b/obj/closestMain.o
--- a/obj/complementMain.o
+++ b/obj/complementMain.o