Strand information from flag

[MuhammedHasan]

Hi,

bamread/bamread/read.py

Line 14 in 4b3d15b

strands = pd.Series(strands).replace({16: "+", 0: "-"}).astype("category")

This line should be like that, isn't it?

strands = pd.Series(strands).replace({0: "+", 16: "-"}).astype("category")

flag 16 means that SEQ being reverse complemented so negative-strand?

https://en.wikipedia.org/wiki/SAM_(file_format)

[endrebak]

Have I made such a fundamental mistake? :(

[endrebak]

This answer seems to agree with you:

The bit for 16 is set if the read is mapped on the reverse strand

[endrebak]

Yikes, you are correct!

[endrebak]

Fixed and uploaded new version to PyPI.