1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
|
#ifndef FREEBAYES_PARAMETERS_H
#define FREEBAYES_PARAMETERS_H
#include <cstdio>
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <map>
#include <getopt.h>
#include <stdlib.h>
#include <fastahack/split.h>
#include "version_git.h"
#include "Utility.h"
using namespace std;
// Encapsulates tracking and parsing of command line program parameters
class Parameters {
friend ostream &operator<<(ostream &out, const Parameters &p);
public:
// i/o parameters:
string bam; // -b --bam
vector<string> bams;
bool useStdin; // -c --stdin
string fasta; // -f --fasta-reference
string targets; // -t --targets
vector<string> regions; // -r --region
string samples; // -s --samples
string populationsFile;
string cnvFile;
//string log;
string output; // -v --vcf
string outputFile;
bool gVCFout; // -l --gvcf
int gVCFchunk;
bool gVCFNoChunk;
string variantPriorsFile;
string haplotypeVariantFile;
bool reportAllHaplotypeAlleles;
bool reportMonomorphic;
bool boundIndels;
bool onlyUseInputAlleles;
string alleleObservationBiasFile;
bool standardGLs;
int baseQualityCap;
double probContamination;
string contaminationEstimateFile;
// operation parameters
bool useDuplicateReads; // -E --use-duplicate-reads
bool suppressOutput; // -S --suppress-output
int useBestNAlleles; // -n --use-best-n-alleles
bool forceRefAllele; // -F --force-reference-allele
bool useRefAllele; // -U --use-reference-allele
bool diploidReference; // -H --haploid-reference
bool allowIndels; // -I --allow-indels
bool leftAlignIndels; // -O --left-align-indels
bool allowMNPs; // -X --allow-mnps
bool allowComplex; // -X --allow-complex
bool strictVCF;
int maxComplexGap;
//int maxHaplotypeLength;
int minRepeatSize;
double minRepeatEntropy;
bool usePartialObservations;
bool allowSNPs; // -I --no-snps
bool pooledDiscrete;
bool pooledContinuous;
bool ewensPriors;
bool permute; // --permute
bool useMappingQuality; //
bool useMinIndelQuality;
bool obsBinomialPriors;
bool alleleBalancePriors;
bool hwePriors;
bool reportGenotypeLikelihoodMax;
int genotypingMaxIterations;
int genotypingMaxBandDepth;
bool excludePartiallyObservedGenotypes;
bool excludeUnobservedGenotypes;
float genotypeVariantThreshold;
int siteSelectionMaxIterations;
bool allSites; // TODO
double limitGL; // minimum GL that is output
int minPairedAltCount;
double minAltMeanMapQ;
int minAltQSum;
int MQR; // -M --reference-mapping-quality
int BQR; // -B --reference-base-quality
int ploidy; // -p --ploidy
int MQL0; // -m --min-mapping-quality
int BQL0; // -q --min-base-quality
int minSupportingMappingQualitySum; // -R --min-supporting-mapping-quality
int minSupportingAlleleQualitySum; // -S --min-supporting-base-quality
int BQL2; // -Q --mismatch-base-quality-threshold
int RMU; // -U --read-mismatch-limit
float readMaxMismatchFraction; // -z --read-max-mismatch-fraction
int readSnpLimit; // -$ --read-snp-limit
int readIndelLimit; // -e --read-indel-limit
int IDW; // -I --indel-exclusion-window
long double TH; // -T --theta
long double PVL; // -P --pvar
// -K --posterior-integration-depth
int posteriorIntegrationDepth;
bool calculateMarginals;
string algorithm;
double RDF; // -D --read-dependence-factor
long double diffusionPriorScalar; // -V --diffusion-prior-scalar
int WB; // -W --posterior-integration-bandwidth
// XXX adjusting this to anything other than 1 may have bad consequences
// for large numbers of samples
int TB; // -Y --posterior-integration-depth
bool includeMonoB;
int TR;
int I;
long double minAltFraction; // -F --min-alternate-fraction
int minAltCount; // -C --min-alternate-count
int minAltTotal; // -G --min-alternate-total
int minCoverage; // -! --min-coverage
int limitCoverage; // -+ --limit-coverage
int skipCoverage; // -g --skip-coverage
int trimComplexTail; // -. --trim-complex-tail
int debuglevel; // -d --debug increments
bool debug; // set if debuglevel >=1
bool debug2; // set if debuglevel >=2
bool showReferenceRepeats;
// functions
Parameters(int argc, char** argv);
void usage(char **argv);
void simpleUsage(char **argv);
// reporting
string commandline;
};
#endif
|