SAM strand suffix optimization

[qiyunzhu]

A SAM file generated from paired-end sequences will have strand suffix (/1 for forward strand, /2 for reverse strand) trimmed (thus the query names are identical), but the strand information will be embeded in the flag (2nd column), an integer in which the 7th bit represents the forward read and the 8th bit represents the reverse read.

For example, flag = 99 (0b1100011) is the forward read, flag = 147 (0b10010011) is the reverse read, flag = 16 (0b10000) is an unpaired sequence.

This information needs to be appended to the query name. Previously, the solution was:

if flag & (1 << 6):
    qname += '/1'
elif flag & (1 << 7):
    qname += '/2'

I tested several solutions. There is an elegant solution, which performs bit operation once and get the correct strand information for both:

if strand := flag >> 6 & 0b11:
    qname = f'{qname}/{strand}'

The variable strand will have three values: 0 for unpaired, 1 for forward, and 2 for reverse.

However, the expensive part is the subsequent string concatenation. I couldn't find a way that is more efficient than the original solution.