Convert MIRA Assembly Format (MAF) to Sequence Alignment/Map (SAM) format
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Tests Added internal switch to force CIGAR strings with M Jun 11, 2012
README README change, should work on MAF files from MIRA 4.0 too. Nov 18, 2013 Fixed typo in README Mar 18, 2015 Cope with gap characters within soft clipped ends of reads. Mar 24, 2015


This is a simple Python script designed to covert from the MIRA
Assembly Format (MAF) to Sequence Alignment/Map (SAM) format.


This Python script served as an interim converter for MAF files from
up to MIRA v3.4 into the popular SAM/BAM assembly/mapping format.
The script was first publicly released on 30 September 2010 on the
MIRA project's mailing list:,13

Please note that the MIRA v3.9.x development releases leading to MIRA v4
have native support for SAM output via the included convert_project tool,
so this script will become obsolete. However, it has been
updated to handle the revised MAF files from MIRA v3.9 and 4.0 as well.

The source code repository for this script is here:

The script requires Biopython to be installed, see