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biopet.biopet
Commits
cf10ac0c
Commit
cf10ac0c
authored
Mar 14, 2016
by
Peter van 't Hof
Browse files
Adding options to freebayes
parent
ad1c8310
Changes
1
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Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
cf10ac0c
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
,
Reference
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Extension for freebayes
...
...
@@ -37,7 +37,93 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
@Output
(
required
=
true
)
var
outputVcf
:
File
=
null
@Input
(
required
=
false
)
var
bam_list
:
Option
[
File
]
=
config
(
"bam_list"
)
@Input
(
required
=
false
)
var
targets
:
Option
[
File
]
=
config
(
"targets"
)
@Input
(
required
=
false
)
var
samples
:
Option
[
File
]
=
config
(
"samples"
)
@Input
(
required
=
false
)
var
populations
:
Option
[
File
]
=
config
(
"populations"
)
@Input
(
required
=
false
)
var
cnv_map
:
Option
[
File
]
=
config
(
"cnv_map"
)
@Input
(
required
=
false
)
var
trace
:
Option
[
File
]
=
config
(
"trace"
)
@Input
(
required
=
false
)
var
failed_alleles
:
Option
[
File
]
=
config
(
"failed_alleles"
)
@Input
(
required
=
false
)
var
observation_bias
:
Option
[
File
]
=
config
(
"observation_bias"
)
@Input
(
required
=
false
)
var
contamination_estimates
:
Option
[
File
]
=
config
(
"contamination_estimates"
)
@Input
(
required
=
false
)
var
variant_input
:
Option
[
File
]
=
config
(
"variant_input"
)
@Input
(
required
=
false
)
var
haplotype_basis_alleles
:
Option
[
File
]
=
config
(
"haplotype_basis_alleles"
)
var
pvar
:
Option
[
Int
]
=
config
(
"pvar"
)
var
theta
:
Option
[
Int
]
=
config
(
"theta"
)
var
ploidy
:
Option
[
Int
]
=
config
(
"ploidy"
)
var
use_best_n_alleles
:
Option
[
Int
]
=
config
(
"use_best_n_alleles"
)
var
max_complex_gap
:
Option
[
Int
]
=
config
(
"max_complex_gap"
)
var
min_repeat_size
:
Option
[
Int
]
=
config
(
"min_repeat_size"
)
var
min_repeat_entropy
:
Option
[
Int
]
=
config
(
"min_repeat_entropy"
)
var
read_mismatch_limit
:
Option
[
Int
]
=
config
(
"read_mismatch_limit"
)
var
read_max_mismatch_fraction
:
Option
[
Int
]
=
config
(
"read_max_mismatch_fraction"
)
var
read_snp_limit
:
Option
[
Int
]
=
config
(
"read_snp_limit"
)
var
read_indel_limit
:
Option
[
Int
]
=
config
(
"read_indel_limit"
)
var
min_alternate_fraction
:
Option
[
Int
]
=
config
(
"min_alternate_fraction"
)
var
min_alternate_count
:
Option
[
Int
]
=
config
(
"min_alternate_count"
)
var
min_alternate_qsum
:
Option
[
Int
]
=
config
(
"min_alternate_qsum"
)
var
min_alternate_total
:
Option
[
Int
]
=
config
(
"min_alternate_total"
)
var
min_coverage
:
Option
[
Int
]
=
config
(
"min_coverage"
)
var
genotyping_max_iterations
:
Option
[
Int
]
=
config
(
"genotyping_max_iterations"
)
var
genotyping_max_banddepth
:
Option
[
Int
]
=
config
(
"genotyping_max_banddepth"
)
var
genotype_variant_threshold
:
Option
[
Int
]
=
config
(
"genotype_variant_threshold"
)
var
read_dependence_factor
:
Option
[
Int
]
=
config
(
"read_dependence_factor"
)
var
min_mapping_quality
:
Option
[
Double
]
=
config
(
"min_mapping_quality"
)
var
min_base_quality
:
Option
[
Double
]
=
config
(
"min_base_quality"
)
var
min_supporting_allele_qsum
:
Option
[
Double
]
=
config
(
"min_supporting_allele_qsum"
)
var
min_supporting_mapping_qsum
:
Option
[
Double
]
=
config
(
"min_supporting_mapping_qsum"
)
var
mismatch_base_quality_threshold
:
Option
[
Double
]
=
config
(
"mismatch_base_quality_threshold"
)
var
base_quality_cap
:
Option
[
Double
]
=
config
(
"base_quality_cap"
)
var
prob_contamination
:
Option
[
Double
]
=
config
(
"prob_contamination"
)
var
stdin
:
Boolean
=
config
(
"stdin"
,
default
=
false
)
var
only_use_input_alleles
:
Boolean
=
config
(
"only_use_input_alleles"
,
default
=
false
)
var
report_all_haplotype_alleles
:
Boolean
=
config
(
"report_all_haplotype_alleles"
,
default
=
false
)
var
report_monomorphic
:
Boolean
=
config
(
"report_monomorphic"
,
default
=
false
)
var
pooled_discrete
:
Boolean
=
config
(
"pooled_discrete"
,
default
=
false
)
var
pooled_continuous
:
Boolean
=
config
(
"pooled_continuous"
,
default
=
false
)
var
use_reference_allele
:
Boolean
=
config
(
"use_reference_allele"
,
default
=
false
)
var
no_snps
:
Boolean
=
config
(
"no_snps"
,
default
=
false
)
var
no_indels
:
Boolean
=
config
(
"no_indels"
,
default
=
false
)
var
no_mnps
:
Boolean
=
config
(
"no_mnps"
,
default
=
false
)
var
no_complex
:
Boolean
=
config
(
"no_complex"
,
default
=
false
)
var
no_partial_observations
:
Boolean
=
config
(
"no_partial_observations"
,
default
=
false
)
var
dont_left_align_indels
:
Boolean
=
config
(
"dont_left_align_indels"
,
default
=
false
)
var
use_duplicate_reads
:
Boolean
=
config
(
"use_duplicate_reads"
,
default
=
false
)
var
standard_filters
:
Boolean
=
config
(
"standard_filters"
,
default
=
false
)
var
no_population_priors
:
Boolean
=
config
(
"no_population_priors"
,
default
=
false
)
var
hwe_priors_off
:
Boolean
=
config
(
"hwe_priors_off"
,
default
=
false
)
var
binomial_obs_priors_off
:
Boolean
=
config
(
"binomial_obs_priors_off"
,
default
=
false
)
var
allele_balance_priors_off
:
Boolean
=
config
(
"allele_balance_priors_off"
,
default
=
false
)
var
legacy_gls
:
Boolean
=
config
(
"legacy_gls"
,
default
=
false
)
var
report_genotype_likelihood_max
:
Boolean
=
config
(
"report_genotype_likelihood_max"
,
default
=
false
)
var
exclude_unobserved_genotypes
:
Boolean
=
config
(
"exclude_unobserved_genotypes"
,
default
=
false
)
var
use_mapping_quality
:
Boolean
=
config
(
"use_mapping_quality"
,
default
=
false
)
var
harmonic_indel_quality
:
Boolean
=
config
(
"harmonic_indel_quality"
,
default
=
false
)
var
genotype_qualities
:
Boolean
=
config
(
"genotype_qualities"
,
default
=
false
)
var
debug
:
Boolean
=
config
(
"debug"
,
default
=
logger
.
isDebugEnabled
)
var
haplotypeLength
:
Option
[
Int
]
=
config
(
"haplotype_length"
)
executable
=
config
(
"exe"
,
default
=
"freebayes"
)
...
...
@@ -52,7 +138,69 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
def
cmdLine
=
executable
+
required
(
"--fasta-reference"
,
reference
)
+
repeat
(
"--bam"
,
bamfiles
)
+
optional
(
"--bam-list"
,
bam_list
)
+
optional
(
"--targets"
,
targets
)
+
optional
(
"--samples"
,
samples
)
+
optional
(
"--populations"
,
populations
)
+
optional
(
"--cnv-map"
,
cnv_map
)
+
optional
(
"--trace"
,
trace
)
+
optional
(
"--failed-alleles"
,
failed_alleles
)
+
optional
(
"--observation-bias"
,
observation_bias
)
+
optional
(
"--contamination-estimates"
,
contamination_estimates
)
+
optional
(
"--variant-input"
,
variant_input
)
+
optional
(
"--haplotype-basis-alleles"
,
haplotype_basis_alleles
)
+
optional
(
"--vcf"
,
outputVcf
)
+
optional
(
"--pvar"
,
pvar
)
+
optional
(
"--theta"
,
theta
)
+
optional
(
"--ploidy"
,
ploidy
)
+
optional
(
"--use-best-n-alleles"
,
use_best_n_alleles
)
+
optional
(
"--max-complex-gap"
,
max_complex_gap
)
+
optional
(
"--min-repeat-size"
,
min_repeat_size
)
+
optional
(
"--min-repeat-entropy"
,
min_repeat_entropy
)
+
optional
(
"--read-mismatch-limit"
,
read_mismatch_limit
)
+
optional
(
"--read-max-mismatch-fraction"
,
read_max_mismatch_fraction
)
+
optional
(
"--read-snp-limit"
,
read_snp_limit
)
+
optional
(
"--read-indel-limit"
,
read_indel_limit
)
+
optional
(
"--min-alternate-fraction"
,
min_alternate_fraction
)
+
optional
(
"--min-alternate-count"
,
min_alternate_count
)
+
optional
(
"--min-alternate-qsum"
,
min_alternate_qsum
)
+
optional
(
"--min-alternate-total"
,
min_alternate_total
)
+
optional
(
"--min-coverage"
,
min_coverage
)
+
optional
(
"--genotyping-max-iterations"
,
genotyping_max_iterations
)
+
optional
(
"--genotyping-max-banddepth"
,
genotyping_max_banddepth
)
+
optional
(
"--genotype-variant-threshold"
,
genotype_variant_threshold
)
+
optional
(
"--read-dependence-factor"
,
read_dependence_factor
)
+
optional
(
"--min-mapping-quality"
,
min_mapping_quality
)
+
optional
(
"--min-base-quality"
,
min_base_quality
)
+
optional
(
"--min-supporting-allele-qsum"
,
min_supporting_allele_qsum
)
+
optional
(
"--min-supporting-mapping-qsum"
,
min_supporting_mapping_qsum
)
+
optional
(
"--mismatch-base-quality-threshold"
,
mismatch_base_quality_threshold
)
+
optional
(
"--base-quality-cap"
,
base_quality_cap
)
+
optional
(
"--prob-contamination"
,
prob_contamination
)
+
conditional
(
only_use_input_alleles
,
"--only-use-input-alleles"
)
+
conditional
(
report_all_haplotype_alleles
,
"--report-all-haplotype-alleles"
)
+
conditional
(
report_monomorphic
,
"--report-monomorphic"
)
+
conditional
(
pooled_discrete
,
"--pooled-discrete"
)
+
conditional
(
pooled_continuous
,
"--pooled-continuous"
)
+
conditional
(
use_reference_allele
,
"--use-reference-allele"
)
+
conditional
(
no_snps
,
"--no-snps"
)
+
conditional
(
no_indels
,
"--no-indels"
)
+
conditional
(
no_mnps
,
"--no-mnps"
)
+
conditional
(
no_complex
,
"--no-complex"
)
+
conditional
(
no_partial_observations
,
"--no-partial-observations"
)
+
conditional
(
dont_left_align_indels
,
"--dont-left-align-indels"
)
+
conditional
(
use_duplicate_reads
,
"--use-duplicate-reads"
)
+
conditional
(
standard_filters
,
"--standard-filters"
)
+
conditional
(
no_population_priors
,
"--no-population-priors"
)
+
conditional
(
hwe_priors_off
,
"--hwe-priors-off"
)
+
conditional
(
binomial_obs_priors_off
,
"--binomial-obs-priors-off"
)
+
conditional
(
allele_balance_priors_off
,
"--allele-balance-priors-off"
)
+
conditional
(
legacy_gls
,
"--legacy-gls"
)
+
conditional
(
report_genotype_likelihood_max
,
"--report-genotype-likelihood-max"
)
+
conditional
(
exclude_unobserved_genotypes
,
"--exclude-unobserved-genotypes"
)
+
conditional
(
use_mapping_quality
,
"--use-mapping-quality"
)
+
conditional
(
harmonic_indel_quality
,
"--harmonic-indel-quality"
)
+
conditional
(
genotype_qualities
,
"--genotype-qualities"
)
+
conditional
(
debug
,
"--debug"
)
+
optional
(
"--haplotype-length"
,
haplotypeLength
)
}
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