fix awk call to add +1 to end position

pdimens · Mar 4, 2025 · e9266e3 · e9266e3
1 parent 48cea2e
commit e9266e3
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/harpy/snakefiles/align_bwa.smk b/harpy/snakefiles/align_bwa.smk
@@ -214,7 +214,7 @@ rule alignment_coverage:
     container:
         None
     shell:
-        "samtools bedcov -c {input.bed} {input.bam} | awk '{{ $5 = $5 / ($3 - $2); print }}' | gzip > {output}"
+        "samtools bedcov -c {input.bed} {input.bam} | awk '{{ $5 = $5 / ($3 + 1 - $2); print }}' | gzip > {output}"
 
 rule report_config:
     input:

diff --git a/harpy/snakefiles/align_ema.smk b/harpy/snakefiles/align_ema.smk
@@ -282,7 +282,7 @@ rule alignment_coverage:
     container:
         None
     shell:
-        "samtools bedcov -c {input.bed} {input.bam} | awk '{{ $5 = $5 / ($3 - $2); print }}' | gzip > {output}"
+        "samtools bedcov -c {input.bed} {input.bam} | awk '{{ $5 = $5 / ($3 + 1 - $2); print }}' | gzip > {output}"
 
 rule barcode_stats:
     input:

diff --git a/harpy/snakefiles/align_strobealign.smk b/harpy/snakefiles/align_strobealign.smk
@@ -205,7 +205,7 @@ rule alignment_coverage:
     container:
         None
     shell:
-        "samtools bedcov -c {input.bed} {input.bam} | awk '{{ $5 = $5 / ($3 - $2); print }}' | gzip > {output}"
+        "samtools bedcov -c {input.bed} {input.bam} | awk '{{ $5 = $5 / ($3 + 1 - $2); print }}' | gzip > {output}"
 
 rule report_config:
     input: