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error in online AUGUSTUS manual

Open krabapple opened this issue 3 years ago • 0 comments

In https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md

It says:

Explanation of the file format of the extrinsic.cfg file. The gff/gtf file containint the hints must contain somewhere in the last column an entry source=?, where ? is one of the source characters listed in the line after [SOURCES] above.

However, the "[SOURCES] above" text is missing. Did you mean to include all of the explanatory text from the default extrinsic.cfg file, but accidentally omitted it? Here is that text:

source of extrinsic information: M manual anchor (required) P protein database hit E est database hit C combined est/protein database hit D Dialign R retroposed genes T transMapped refSeqs

[SOURCES] M RM

individual_liability: Only unsatisfiable hints are disregarded. By default this flag is not set and the whole hint group is disregarded when one hint in it is unsatisfiable.

[SOURCE-PARAMETERS] T individual_liability

feature bonus malus gradelevelcolumns r+/r-

the gradelevel colums have the following format for each source sourcecharacter numscoreclasses boundary ... boundary gradequot ... gradequot

[GENERAL] start 1 1 M 1 1e+100 RM 1 1 stop 1 1 M 1 1e+100 RM 1 1 tss 1 1 M 1 1e+100 RM 1 1 tts 1 1 M 1 1e+100 RM 1 1 ass 1 1 M 1 1e+100 RM 1 1 dss 1 1 M 1 1e+100 RM 1 1 exonpart 1 1 M 1 1e+100 RM 1 1 exon 1 1 M 1 1e+100 RM 1 1 intronpart 1 1 M 1 1e+100 RM 1 1 intron 1 1 M 1 1e+100 RM 1 1 CDSpart 1 1 M 1 1e+100 RM 1 1 CDS 1 1 M 1 1e+100 RM 1 1 UTRpart 1 1 M 1 1e+100 RM 1 1 UTR 1 1 M 1 1e+100 RM 1 1 irpart 1 1 M 1 1e+100 RM 1 1 nonexonpart 1 1 M 1 1e+100 RM 1 1.15 genicpart 1 1 M 1 1e+100 RM 1 1

Explanation:

The gff/gtf file containing the hints must contain somewhere in the last column an entry source=?, where ? is one of the source characters listed in the line after [SOURCES] above. ETC...

I still don't understand what 'RM' means, though.

krabapple avatar Jun 10 '21 18:06 krabapple