fix: unmapped reads are ignored, no longer cause length-check crash; version -> 2.9.1

Author: cschu

gffquant/__init__.py

@@ -1,3 +1,3 @@
 """ module docstring """
 
-__version__ = "2.9"
+__version__ = "2.9.1"

gffquant/alignment/bamreader.py

@@ -17,17 +17,26 @@
 
 class SamFlags:
     PAIRED = 0x1
+    PROPERLY_PAIRED = 0x2
+    UNMAPPED = 0x4
     MATE_UNMAPPED = 0x8
     REVERSE = 0x10
+    MATE_REVERSE = 0x20
     FIRST_IN_PAIR = 0x40
     SECOND_IN_PAIR = 0x80
     SECONDARY_ALIGNMENT = 0x100
+    QUAL_CHECK_FAILURE = 0x200
+    PCR_OPTICAL_DUPLICATE = 0x400
     SUPPLEMENTARY_ALIGNMENT = 0x800
 
     @staticmethod
     def is_reverse_strand(flag):
         return bool(flag & SamFlags.REVERSE)
 
+    @staticmethod
+    def is_unmapped(flag):
+        return bool(flag & SamFlags.UNMAPPED)
+
 
 class CigarOps:
     CIGAR_OPS = "MIDNSHP=X"

gffquant/alignment/pysam_alignment_processor.py

@@ -2,7 +2,7 @@
 
 import pysam
 
-from .bamreader import BamAlignment
+from .bamreader import BamAlignment, SamFlags
 
 
 class AlignmentProcessor:
@@ -69,6 +69,9 @@ def get_alignments(
                     dict(pysam_aln.tags)
                 )
 
+                if SamFlags.is_unmapped(aln.flag):
+                    continue
+
                 if aln.flag & filter_flags:
                     continue