Mercurial > repos > devteam > freebayes
changeset 15:59731e950e23 draft
Fix some options.
| author | soranzo |
|---|---|
| date | Fri, 29 Aug 2014 12:15:44 -0400 |
| parents | 443ccd9208a0 |
| children | 6d9407020066 |
| files | freebayes.xml |
| diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/freebayes.xml Fri Jun 20 17:19:11 2014 -0400 +++ b/freebayes.xml Fri Aug 29 12:15:44 2014 -0400 @@ -119,7 +119,7 @@ ${options_type.allele_scope.u} -n "${options_type.allele_scope.n}" --haplotype-length "${options_type.allele_scope.haplotype_length}" - --min-repeat-length "${options_type.allele_scope.min_repeat_length}" + --min-repeat-size "${options_type.allele_scope.min_repeat_length}" --min-repeat-entropy "${options_type.allele_scope.min_repeat_entropy}" ${options_type.allele_scope.no_partial_observations} #end if @@ -166,13 +166,13 @@ #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "True": --base-quality-cap "${$options_type.genotype_likelihoods.base_quality_cap}" ${$options_type.genotype_likelihoods.experimental_gls} - --prob_contamination "${$options_type.genotype_likelihoods.prob_contamination}" + --prob-contamination "${$options_type.genotype_likelihoods.prob_contamination}" #end if ## ALGORITHMIC FEATURES #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "True": - v + ${options_type.algorithmic_features.report_genotype_likelihood_max} -B "${options_type.algorithmic_features.B}" --genotyping-max-banddepth "${options_type.algorithmic_features.genotyping_max_banddepth}" -W "${options_type.algorithmic_features.W}" @@ -375,16 +375,16 @@ <!-- allelic scope --> <conditional name="allele_scope"> - <param name="allele_scope_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set allelic scope?" help="Sets -I, i, -X, -u, -n, -E, --haplotype-length, --min-repeat-length, --min-repeat-entropy, and --no-partial-observations options " /> + <param name="allele_scope_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Set allelic scope?" help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options " /> <when value="set"> <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles" help="-I --no-snps; default=False" /> <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles" help="-i --no-indels; default=False" /> <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs" help="-X --no-mnps; default=False" /> <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)." help="-u --no-complex; default=False" /> <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate" help="-n --use-best-n-alleles; default=0 (all). Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" /> - <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" help="--haplotype-length; default=3." /> - <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp" help="--min-repeat-length; default=5." /> - <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" help="--min-repeat-entrpy; default=0 (off)." /> + <param name="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" help="-E --max-complex-gap --haplotype-length; default=3." /> + <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp" help="--min-repeat-size; default=5." /> + <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" help="--min-repeat-entropy; default=0 (off)." /> <param name="no_partial_observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="False" label="Exclude observations which do not fully span the dynamically-determined detection window" help="--no-partial-observations; default=use all observations, dividing partial support across matching haplotypes when generating haplotypes. " /> </when> <when value="do_not_set"> @@ -463,7 +463,7 @@ <!-- algorithmic features --> <conditional name="algorithmic_features"> - <param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak agrithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options " /> + <param name="algorithmic_features_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Tweak algorithmic features?" help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options " /> <when value="set"> <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." help="--report-genotype-likelihood-max; default=False" /> <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." /> @@ -680,7 +680,7 @@ --haplotype-length N Allow haplotype calls with contiguous embedded matches of up to this length. (default: 3) - --min-repeat-length N + --min-repeat-size N When assembling observations across repeats, require the total repeat length at least this many bp. (default: 5) --min-repeat-entropy N