Add different modes to BamWriter.Open

[1dayac]

Hello, Jeremiah!
I use SeqLib and bxtools in my research really extensively, thank you a lot:)
Is it possible to add "append" mode for BamWriter.Open function? I faced a problem when this is an only fast solution requires opening bam-files multiple times.

Thanks,
Dima

[walaj]

Thanks!
Could you describe more what you mean by append? BamWriter is read-only for BAMs. Is there an append functionality in htslib you are thinking of?

[1dayac]

I have bam-file a.bam. Imagine that I want to add several records from the b.bam. Now I can't do something like writer.Open("a.bam", 'a') because BamWriter doesn't have an interface like this and just opening the file will overwrite it. Htslib has append functionality and I was able to change the code to do it in a forked version (you can take a look), but I'm just slightly familiar with the SeqLib code and it is definitely a workaround Dima вс, 26 авг. 2018 г. в 19:36, Jeremiah Wala <notifications@github.com>:

…

Thanks! Could you describe more what you mean by append? BamWriter is read-only for BAMs. Is there an append functionality in htslib you are thinking of? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#26 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFT9rXlshx2QrXbLDeYAV5suzGMTwFGbks5uUzD5gaJpZM4WIpxB> .