Author: Michael R. Crusoe <crusoe@ucdavis.edu>
Description: Fix spelling erorr
--- macs2.orig/MACS2/PeakModel.pyx
+++ macs2/MACS2/PeakModel.pyx
@@ -559,7 +559,7 @@
     This method is based on the convolution of a scaled window with the signal.
     The signal is prepared by introducing reflected copies of the signal 
     (with the window size) in both ends so that transient parts are minimized
-    in the begining and end part of the output signal.
+    in the beginning and end part of the output signal.
     
     input:
         x: the input signal 
--- macs2.orig/bin/macs2
+++ macs2/bin/macs2
@@ -370,7 +370,7 @@
     """Add function 'peak calling on bedGraph' argument parsers.
     """    
     argparser_bdgpeakcall = subparsers.add_parser( "bdgpeakcall",
-                                                   help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+                                                   help = "Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
     argparser_bdgpeakcall.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
                                         help = "MACS score in bedGraph. REQUIRED" )
     argparser_bdgpeakcall.add_argument( "-c", "--cutoff" , dest = "cutoff", type = float,
@@ -395,7 +395,7 @@
     """Add function 'broad peak calling on bedGraph' argument parsers.
     """
     argparser_bdgbroadcall = subparsers.add_parser( "bdgbroadcall",
-                                                    help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+                                                    help = "Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
     argparser_bdgbroadcall.add_argument( "-i", "--ifile", dest = "ifile" , type = str, required = True,
                                          help = "MACS score in bedGraph. REQUIRED" )
     argparser_bdgbroadcall.add_argument( "-c", "--cutoff-peak", dest = "cutoffpeak", type = float,
@@ -418,7 +418,7 @@
     """Add function 'peak calling on bedGraph' argument parsers.
     """
     argparser_bdgcmp = subparsers.add_parser( "bdgcmp",
-                                              help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+                                              help = "Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
     argparser_bdgcmp.add_argument( "-t", "--tfile", dest = "tfile", type = str, required = True,
                                    help = "Treatment bedGraph file, e.g. *_treat_pileup.bdg from MACSv2. REQUIRED")
     argparser_bdgcmp.add_argument( "-c", "--cfile", dest = "cfile", type = str, required = True,
@@ -444,7 +444,7 @@
     """Add function 'operations on score column of bedGraph' argument parsers.
     """    
     argparser_bdgopt = subparsers.add_parser( "bdgopt",
-                                              help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+                                              help = "Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
     argparser_bdgopt.add_argument( "-i", "--ifile", dest = "ifile", type = str, required = True,
                                    help = "MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE genome. REQUIRED" )
     argparser_bdgopt.add_argument( "-m", "--method", dest = "method", type = str,
@@ -461,7 +461,7 @@
     """Add function 'combine replicates' argument parsers.
     """
     argparser_cmbreps = subparsers.add_parser( "cmbreps",
-                                               help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+                                               help = "Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
     argparser_cmbreps.add_argument( "-i", dest = "ifile", type = str, required = True, nargs = "+",
                                     help = "MACS score in bedGraph for each replicate. Require exactly two files such as '-i A B'. REQUIRED" )
     # argparser_cmbreps.add_argument( "-w", dest = "weights", type = float, nargs = "*",
@@ -503,7 +503,7 @@
     
 def add_bdgdiff_parser( subparsers ):
     argparser_bdgdiff = subparsers.add_parser( "bdgdiff",
-                                               help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continous so only bedGraph files from MACS2 are accpetable." )
+                                               help = "Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable." )
     argparser_bdgdiff.add_argument( "--t1", dest = "t1bdg", type = str, required = True,
                                     help = "MACS pileup bedGraph for condition 1. Incompatible with callpeak --SPMR output. REQUIRED" )
     argparser_bdgdiff.add_argument( "--t2", dest="t2bdg", type = str, required = True,
