Fix misc bugs

* Specify matplotlib as dependency * Skip mappings without NM tag * Git ignore pycache
Swart-lab · Apr 5, 2022 · c28b94e · c28b94e
1 parent d206041
commit c28b94e
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+mnutils/__pycache__
diff --git a/env.yml b/env.yml
@@ -7,3 +7,4 @@ dependencies:
   - samtools=1.10
   - pysam=0.16.0.1
   - biopython=1.77
+  - matplotlib>=3.1.1
diff --git a/mnutils/Posmap.py b/mnutils/Posmap.py
@@ -103,6 +103,7 @@ def read_bam(self, bamfile,
         for read in bamiter:
             if (not read.is_secondary and
                     not read.is_duplicate and
+                    read.has_tag('NM') and
                     read.get_tag("NM") <= 1):
                 # TODO: Mismatches should actually be summed for each read PAIR,
                 # not for each read segment as is currently done here