[ensembl-dev] blastz-chain-net axtChain linearGap option

[Sharon Wei]

> Dear Ensemblers,
>
> I recently updated ensemlb-compara WGA pipeline and found there was a 
> change in axtChain command.
> Now it is used with option "-linearGap=medium" and by axtChain 
> document, medium should be a file name, however I do not find that 
> file in the ensembl-compara package. What I did to make the job run is 
> creating a file named 'medium' by copying the content of the following 
> sample linearGap file. However, just to be careful, I want to get some 
> expert's opinion on whether that is O.K. and what is the rational on 
> behind adding the new option.
>
>
> axtChain
> axtChain - Chain together axt alignments.
> usage:
>    axtChain in.axt tNibDir qNibDir out.chain
> Where tNibDir/qNibDir are either directories full of nib files, or the
> name of a .2bit file
> options:
>    -psl Use psl instead of axt format for input
>    -faQ qNibDir is a fasta file with multiple sequences for query
>    -faT tNibDir is a fasta file with multiple sequences for query
>    -minScore=N  Minimum score for chain, default 1000
>    -details=fileName Output some additional chain details
>    -scoreScheme=fileName Read the scoring matrix from a blastz-format 
> file
>    -linearGap=filename Read piecewise linear gap from tab delimited file
>    sample linearGap file
> tablesize 11
> smallSize 111
> position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
> qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
> tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900
> bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300
>
>
> Thanks,
>
> Sharon