simplify it

pdimens · May 10, 2024 · bccdc06 · bccdc06
1 parent 789642b
commit bccdc06
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diff --git a/src/harpy/scripts/filterBXBAM.py b/src/harpy/scripts/filterBXBAM.py
diff --git a/src/harpy/scripts/separateValidBX b/src/harpy/scripts/separateValidBX
@@ -0,0 +1,9 @@
+#! /usr/bin/env bash
+
+if [[ -z "$1" ]]; then
+    echo -e "\n  Split a BAM file with BX:Z tags into 2 files, one with valid ACBD barcodes (stdout), one with invalid ACBD barcodes (stderr)."
+    echo -e "\n [usage] separateValidBX input.bam > valid.bam 2> invalid.bam"
+    exit
+fi
+
+samtools view -e '[BX]!~"[ABCD]0{2,4}"' --unoutput /dev/stderr $1