Opened 16 years ago
Closed 16 years ago
#174 closed defect (fixed)
Phylip.eft, missing line break
| Reported by: | fog | Owned by: | devel |
|---|---|---|---|
| Priority: | critical | Milestone: | |
| Component: | no idea | Version: | SVN |
| Keywords: | Cc: | epruesse@… |
Description
When exporting sequences using phylip.eft there is a line break missing in the first line: 10643 1393DdeBacte AUUGAACGCU GGCGGCAUGC CUUACACAUG CAAGUCGAAC GGCACGCUUC Correct: 10643 1393 DdeBacte? AUUGAACGCU GGCGGCAUGC CUUACACAUG CAAGUCGAAC GGCACGCUUC
Unforntunately I do not understand how the conversion from genbank to phylip is done by the exporter. This export function is crucial for external programs like PhyMl? and RaxMl?
Attachments (1)
Change History (4)
Changed 16 years ago by epruesse
comment:1 Changed 16 years ago by epruesse
comment:2 Changed 16 years ago by meierh
Sorry to correct here: This occurs only when the number of OTUs exported increases 9999.
comment:3 Changed 16 years ago by westram
- Resolution set to fixed
- Status changed from new to closed
- fixed by [5957] (based on attached patch)
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This happens when the number of columns exportet is > 9999. CONVERTALN reserves 4 bytes of space for this number in the first line. If it is larger than 9999 the \n will be overwritten.
The attached patch changes this to reserve 8 bytes. I would suggest to defer an actual fix of this questionable practice until after the release.