HI，

I want to get following fields from a bam file:

• Read_length
• Alignment_length
• Edit_distance

I known I can get this fields from pysam, But I want to do this step with shell, I have the following scheme

• Read_length use awk calculate length of reads
• Alignment_length use awk calculate MD fields?
• Edit_distance get from NM fields

I'm not sure if my understanding of Alignment length is correct, how should I get this information correctly?

for example, if I have a MD field:

10A3T0T10

So is the alignment length is

10+1(A)+3+1(T)+0+1(T)+10

but if we have

10A^3T0T10

here is also alignment length is 10+1(A)+3+1(T)+0+1(T)+10 or 10+1(A)+1(^)+3+1(T)+0+1(T)+10, The read.query_alignment_length in pysam output as same as previous

update:

Can I use read.query_alignment_length in pysam to get alignment length?