From 58a71439a9f1039d2472ddf1b7bc421d195b2140 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 3 Sep 2018 18:08:03 +0200
Subject: [PATCH] Factorized code (MAPQ filtering, RPK, rTRPM).
---
libhts/libhts.py | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/libhts/libhts.py b/libhts/libhts.py
index d73e512..d4a6601 100644
--- a/libhts/libhts.py
+++ b/libhts/libhts.py
@@ -268,6 +268,25 @@ def make_seeding_function(seeding_string):
return seeding_function
+def aligner2min_mapq(aligner, wildcards):
+ """
+ Option to filter on MAPQ value in featureCounts.
+
+ What minimal MAPQ value should a read have to be considered uniquely mapped?
+ See <https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/>.
+ """
+ mapped_type = wildcards.mapped_type
+ if mapped_type.startswith("unique_"):
+ if aligner == "hisat2":
+ return "-Q 60"
+ elif aligner == "bowtie2":
+ return "-Q 23"
+ else:
+ raise NotImplementedError(f"{aligner} not handled (yet?)")
+ else:
+ return ""
+
+
## Not sure this is a good idea...
# def masked_gmean(a, axis=0, dtype=None):
# """Modified from stats.py."""
--
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