merge rules isbpsort and split into on single rule bam2bed

rules/preprocessISBP.smk

@@ -9,21 +9,22 @@ rule filterBam:
 rule bam2bed:
 	message: "Convert Filtered BAM file into BED"
 	input: config['results']+"/1.filteredISBPs.bam"
-	output: config['results']+"/1.filteredISBPs.bed"
-	log: config['results']+"/2.bam2bed.log"
-	shell: "bamToBed -i {input} |sort -k1,1 -k2,2n  1> {output} 2> {log}"
+	output: config['results']+"/1.filteredISBPs/{chrom}/sorted.bed"
+	log: config['results']+"/1.filteredISBPs/{chrom}/sorted.log"
+        params: 'Chr{chrom}'
+	shell: "bamToBed -i {input} |fgrep -i {params}|cut -d ':' -f 1|sort -k1,1 -k2,2n  1> {output} 2> {log}"
 
 
-rule dumpISBPsID:
-	message: "Dump ISBPs IDs"
-	input: config['results']+"/1.filteredISBPs.bed"
-	output: config['results']+"/1.filteredISBPs.ids"
-	shell: " cut -f 4 {input} > {output}"
+#rule dumpISBPsID:
+#	message: "Dump ISBPs IDs"
+#	input: config['results']+"/1.filteredISBPs.bed"
+#	output: config['results']+"/1.filteredISBPs.ids"
+#	shell: " cut -f 4 {input} > {output}"
 
-rule splitISBP:
-	message: "Split isbps per chromosome"
-	input: config['results']+"/1.filteredISBPs.bed"
-	output: config['results']+"/1.filteredISBPs/{chrom}/sorted.bed"
-	log: config['results']+"/1.filteredISBPs/{chrom}/sorted.log"
-	params: 'Chr{chrom}'
-	shell: "fgrep -i {params} {input} 1> {output} 2> {log}"
+#rule splitISBP:
+#	message: "Split isbps per chromosome"
+#	input: config['results']+"/1.filteredISBPs.bed"
+#	output: config['results']+"/1.filteredISBPs/{chrom}/sorted.bed"
+#	log: config['results']+"/1.filteredISBPs/{chrom}/sorted.log"
+#	params: 'Chr{chrom}'
+#	shell: "fgrep -i {params} {input} 1> {output} 2> {log}"