Documentation ¶
Overview ¶
Package cmd provides implementations for the elprep command line.
Index ¶
Constants ¶
const BedToElsitesHelp = "\nbed-to-elsites parameters:\n" +
"elprep bed-to-elsites bed-file elsites-file\n" +
"[--log-path path]\n"
BedToElsitesHelp is the help string for this command.
const CombinedSfmFilterHelp = "filter/sfm parameters:\n" +
"elprep [filter | sfm] sam-file sam-output-file\n" +
"[--output-type [sam | bam]]\n" +
"[--replace-reference-sequences sam-file]\n" +
"[--filter-unmapped-reads]\n" +
"[--filter-unmapped-reads-strict]\n" +
"[--filter-mapping-quality mapping-quality]\n" +
"[--filter-non-exact-mapping-reads]\n" +
"[--filter-non-exact-mapping-reads-strict]\n" +
"[--filter-non-overlapping-reads bed-file]\n" +
"[--replace-read-group read-group-string]\n" +
"[--mark-duplicates]\n" +
"[--mark-optical-duplicates file]\n" +
"[--optical-duplicates-pixel-distance nr]\n" +
"[--remove-duplicates]\n" +
"[--remove-optional-fields [all | list]]\n" +
"[--keep-optional-fields [none | list]]\n" +
"[--sorting-order [keep | unknown | unsorted | queryname | coordinate]]\n" +
"[--clean-sam]\n" +
"[--bqsr recal-file]\n" +
"[--reference elfasta]\n" +
"[--quantize-levels nr]\n" +
"[--sqq list]\n" +
"[--max-cycle nr]\n" +
"[--known-sites list]\n" +
"[--haplotypecaller vcf-file]\n" +
"[--reference-confidence [GVCF | BP_RESOLUTION | NONE]\n" +
"[--sample-name sample-name]\n" +
"[--activity-profile igv-file]\n" +
"[--assembly-regions igv-file]\n" +
"[--assembly-region-padding nr]\n" +
"[--target-regions bed-file]\n" +
"[--nr-of-threads nr]\n" +
"[--timed]\n" +
"[--log-path path]\n" +
"[--intermediate-files-output-prefix name] (sfm only)\n" +
"[--intermediate-files-output-type [sam | bam]] (sfm only)\n" +
"[--tmp-path path]\n" +
"[--single-end] (sfm only)\n" +
"[--contig-group-size nr] (sfm only)\n"
CombinedSfmFilterHelp is a help string that combines the help strings for the filter and sfm commands.
const FastaToElfastaHelp = "fasta-to-elfasta parameters:\n" +
"elprep fasta-to-elfasta fasta-file elfasta-file\n" +
"[--log-path path]\n"
FastaToElfastaHelp is the help string for this command.
const FilterExtendedHelp = FilterHelp +
"[--mark-optical-duplicates-intermediate file]\n" +
"[--bqsr-tables-only table-file]\n" +
"[--bqsr-apply path]\n" +
"[--recal-file file]\n" +
"[--spread-file file]\n" +
"[--pg-cmd-line cmd]\n"
FilterExtendedHelp is the extended help string for this command.
const FilterHelp = "\nfilter parameters:\n" +
"elprep filter sam-file sam-output-file\n" +
"[--output-type [sam | bam]]\n" +
"[--replace-reference-sequences sam-file]\n" +
"[--filter-unmapped-reads]\n" +
"[--filter-unmapped-reads-strict]\n" +
"[--filter-mapping-quality mapping-quality]\n" +
"[--filter-non-exact-mapping-reads]\n" +
"[--filter-non-exact-mapping-reads-strict]\n" +
"[--filter-non-overlapping-reads bed-file]\n" +
"[--replace-read-group read-group-string]\n" +
"[--mark-duplicates]\n" +
"[--mark-optical-duplicates file]\n" +
"[--optical-duplicates-pixel-distance nr]\n" +
"[--remove-duplicates]\n" +
"[--remove-optional-fields [all | list]]\n" +
"[--keep-optional-fields [none | list]]\n" +
"[--sorting-order [keep | unknown | unsorted | queryname | coordinate]]\n" +
"[--clean-sam]\n" +
"[--reference elfasta]\n" +
"[--bqsr recal-file]\n" +
"[--quantize-levels nr]\n" +
"[--sqq list]\n" +
"[--max-cycle nr]\n" +
"[--known-sites list]\n" +
"[--haplotypecaller vcf-file]\n" +
"[--reference-confidence [GVCF | BP_RESOLUTION | NONE]\n" +
"[--sample-name sample-name]\n" +
"[--activity-profile igv-file]\n" +
"[--assembly-regions igv-file]\n" +
"[--assembly-region-padding nr]\n" +
"[--target-regions]\n" +
"[--nr-of-threads nr]\n" +
"[--timed]\n" +
"[--log-path path]\n"
FilterHelp is the help string for this command.
const HelpMessage = "Print command details:\n" +
"[--help]\n" +
"[--help-extended]\n"
HelpMessage is printed to show the --help and --help-extended flags
const MergeHelp = "\nmerge parameters:\n" +
"elprep merge /path/to/input sam-output-file\n" +
"[--output-type [sam | bam]]\n" +
"[--single-end]\n" +
"[--ignore-spread-file] \n" +
"[--nr-of-threads n]\n" +
"[--timed]\n" +
"[--log-path path]\n"
MergeHelp is the help string for this command.
const MergeOpticalDuplicatesMetricsHelp = "\nmerge-optical-duplicates-metrics parameters:\n" +
"elprep merge-optical-duplicates-metrics sam-input-file sam-output-file metrics-file /path/to/intermediate/metrics\n" +
"[--remove-duplicates]\n" +
"[--nr-of-threads nr]\n" +
"[--timed]\n" +
"[--log-path path]\n"
MergeOpticalDuplicatesMetricsHelp is the help string for this command.
const SfmHelp = "\nsfm parameters:\n" +
"elprep sfm sam-file sam-output-file\n" +
"[--output-type [sam | bam]]\n" +
"[--replace-reference-sequences sam-file]\n" +
"[--filter-unmapped-reads]\n" +
"[--filter-unmapped-reads-strict]\n" +
"[--filter-mapping-quality mapping-quality]\n" +
"[--filter-non-exact-mapping-reads]\n" +
"[--filter-non-exact-mapping-reads-strict]\n" +
"[--filter-non-overlapping-reads bed-file]\n" +
"[--replace-read-group read-group-string]\n" +
"[--mark-duplicates]\n" +
"[--mark-optical-duplicates file]\n" +
"[--optical-duplicates-pixel-distance nr]\n" +
"[--remove-duplicates]\n" +
"[--remove-optional-fields [all | list]]\n" +
"[--keep-optional-fields [none | list]]\n" +
"[--sorting-order [keep | unknown | unsorted | queryname | coordinate]]\n" +
"[--clean-sam]\n" +
"[--bqsr]\n" +
"[--reference elfasta]\n" +
"[--quantize-levels nr]\n" +
"[--sqq list]\n" +
"[--max-cycle nr]\n" +
"[--known-sites list]\n" +
"[--haplotypecaller vcf-file]\n" +
"[--reference-confidence [GVCF | BP_RESOLUTION | NONE]\n" +
"[--sample-name sample-name]\n" +
"[--activity-profile igv-file]\n" +
"[--assembly-regions igv-file]\n" +
"[--assembly-region-padding nr]\n" +
"[--target-regions bed-file]\n" +
"[--nr-of-threads nr]\n" +
"[--timed]\n" +
"[--log-path path]\n" +
"[--intermediate-files-output-prefix name]\n" +
"[--intermediate-files-output-type [sam | bam]]\n" +
"[--tmp-path path]\n" +
"[--single-end]\n" +
"[--contig-group-size nr]\n"
SfmHelp is the help string for this command.
const SplitHelp = "\nsplit parameters:\n" +
"elprep split (sam-file | /path/to/input/) /path/to/output/\n" +
"[--output-prefix name]\n" +
"[--output-type [sam | bam]]\n" +
"[--single-end]\n" +
"[--nr-of-threads nr]\n" +
"[--timed]\n" +
"[--log-path path]\n" +
"[--contig-group-size nr]\n"
SplitHelp is the help string for this command.
const VcfToElsitesHelp = "vcf-to-elsites parameters:\n" +
"elprep vcf-to-elsites vcf-file elsites-file\n" +
"[--log-path path]\n"
VcfToElsitesHelp is the help string for this command.
Variables ¶
var ProgramMessage string
ProgramMessage is the first line printed when the elprep binary is called.
Functions ¶
func FastaToElfasta ¶
func FastaToElfasta()
FastaToElfasta implements the elprep fasta-to-elfasta command.
func MergeOpticalDuplicatesMetrics ¶
func MergeOpticalDuplicatesMetrics()
Merge implements the elprep merge command.
Types ¶
This section is empty.