no mapping quality in final Sam file

benedictpaten / marginAlign

UCSC Nanopore

MIT License

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no mapping quality in final Sam file #19

Closed lfaino closed 8 years ago

lfaino commented 9 years ago

Hi all, I have an issue when I run marginAlign. The first sam file contains the mapping quality (all of them are 255) while the last sam file all the quality goes to 0. how can I fix this problem? are you thinking to fix in a next release?

thanks Luigi

mitenjain commented 8 years ago

Hi Luigi,

We are planning on including a BAQ type score in the next release. This is coming shortly, over the next few weeks.

Thank you.

Best regards, Miten