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mikolmogorov / maf2synteny

A tool for recovering synteny blocks from multiple alignment
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Compatibility with a future change in the output of SibeliaZ #2

Closed iminkin closed 2 years ago

iminkin commented 2 years ago

Right now SibeliaZ's GFF output does not comply strictly with the format spec. I am going to make it compliant in the next releases. The only difference that seems to matter for maf2synteny is that the ID attribute will be spelled in upper-case as in the specification (right now SibeliaZ outputs 'id' in lower-case). Please add support to the ID spelled this way. An example of the output file is here.

In addition, SibeliaZ will output sizes of the input sequences as pragma (as suggested by this issue). It should simplify the computation of the coverage and maybe some other operations.

mikolmogorov commented 2 years ago

Should now be fixed in release 1.1

ghost commented 2 years ago

Fix a bug which outputs incorrect nucLength, see #3 .

mikolmogorov commented 2 years ago

@16m thanks, merged the changes and bumped the 1.2 release