Sort by name to make WASP/Hornet work way better

Hornet assumes that the remapped file is sorted by name, and I had
assumed that by just taking the output of the mapper it would stay that
way, but this later assumption was not justified...

Author: petercombs

Snakefile

@@ -405,7 +405,7 @@ rule wasp_remap:
 rule wasp_keep:
     input:
         toremap="{file}.to.remap.bam",
-        remapped="{file}.remap.bam",
+        remapped="{file}.remap.namesorted.bam",
     output:
         temp("{file}.remap.kept.bam"),
     shell: """
@@ -962,6 +962,17 @@ rule sort_bam:
     samtools sort -o {output} --threads {threads} {input}
     """
 
+
+rule name_sort_bam:
+    input: "{sample}.bam"
+    output: "{sample}.namesorted.bam"
+    log: "{sample}.sorted.log"
+    threads: 4
+    shell: """{module}; module load samtools
+    samtools sort -n -o {output} --threads {threads} {input}
+    """
+
+
 rule index_bam:
     input: "{sample}.bam"
     output: "{sample}.bam.bai"