Removed BIgWig requirement and generate own signal file

HMMRATAC_Guide.txt

@@ -63,7 +63,9 @@ To retrieve the file, for H. sapiens, use the following command:
 
  $ mysql –-user=genome --host=genome-mysql.cse.ucsc.edu –A –e \ “select chrom, size from hg19.chromInfo” > hg19.genome 
 
-4) The final required file that is necessary to run HMMR is a BigWig file containing the 
+4) **NOTE**: This is no longer required as of version 1.2
+
+The final required file that is necessary to run HMMR is a BigWig file containing the 
 genome-wide coverage of ATAC-seq reads. This can be created using multiple programs. One 
 such method is to use bedtools. Use the bedtools “bamtobed” command as follows:
 
@@ -107,7 +109,7 @@ Section 2: Overview of Options
  as described in section 1.3
 
  -w , --wig <BigWig> This is the genome-wide BigWig file created as 
- described in section 1.4
+ described in section 1.4 **NOTE**: This is no longer required as of version 1.2
 
  Optional Parameters:
 

README.md

@@ -2,18 +2,15 @@
 
 Quick Start:
 
-$ sh Make_HMMR_Files.sh ExampleFile.bam hg19.genome ExampleFile.processed
+$ samtools ExampleFile.bam  -o ExampleFile.sorted.bam
 
-$ java -jar HMMRATAC_V1.0_exe.jar -b ExampleFile.processed.bam -i ExampleFile.processed.bam.bai -g hg19.genome -w ExampleFile.processed_fromBedtools.bw 
+$ samtools index ExampleFile.sorted.bam ExampleFile.sorted.bam.bai
 
-The above command uses the bedtools-generated bigWig file. This may not be ideal (See section 1.4 of HMMRATAC_Guide.txt). 
-The better way is to use the bigWig file generated by MACS2. If you have MACS2 installed, the resulting bigWig is created by 
-Make_HMMR_Files.sh.
+$ java -jar HMMRATAC_V1.2_exe.jar -b ExampleFile.sorted.bam -i ExampleFile.sorted.bam.bai -g hg19.genome
+
+**NOTE: Earlier versions of HMMRATAC require a bigwig file. See HMMRATAC_Guide.txt for more detail**
 
-$ java -jar HMMRATAC_V1.0_exe.jar -b ExampleFile.processed.bam -i ExampleFile.processed.bam.bai -g hg19.genome -w ExampleFile.processed_fromMACS2.bw
-
-To use Make_HMMR_Files.sh, you must have samtools, UCSC's bedGraphToBigWig and either bedtools or macs2 installed. Please open the file
-and insert the correct path to each required tool. Alternatively, you can manually create the required input files (See section 1 of HMMRATAC_Guide.txt). 
+Samtools can be downloaded here: http:https://www.htslib.org/download/
 
 Be sure to run HMMRATAC using the executable file, found here: 
 https://github.com/LiuLabUB/HMMRATAC/releases