Removed old flags from cli page

website/docs/cli.md

@@ -132,129 +132,3 @@ Force assemble all windows
 
 ### `--no-contig-check`
 Skip contig check with reference
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-***old***
-### `--min-trim-qual`
-This allows you to define the minimum base quality for trimming 5' and 3' read bases. If this option is not used, the minimum base quality will be defaulted to 10.
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-### `-q`, `--min-base-qual`
-This allows you to define the minimum base quality for SNV calling. If this option is not used, the minimum base quality will be defaulted to 17.
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-### `-Q`, `--min-mapping-qual`
-This allows you to define the minimum mapping quality required to use a read. By default, this value will be set to 15.
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-### `--max-rpt-mismatch`
-This allows you to define the maximum number of mismatches used to detect approximate repeats. By default, the maximum number of mismatches is set to 2.
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-### `--max-tip-length`
-This will define the maximum tip length allowed in the genereated graphs. By default, the maximum tip length is set to 11.
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-### `--graph-traversal-limit`
-Maximum allowed tip length in the graph. By default, this value is set to 11.
-Check cli.cpp, why is params->minGraphTipLength
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-### `--graph-traversal-limit`
-Max BFS/DFS graph traversal limit. By default, this value is set to 100000.
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-### `--max-indel-length`
-Maximum limit on the indel length to detect. Default is set to 500.
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-### `--min-anchor-cov`
-Minimum coverage for anchor nodes (source & sink). Default is 5
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-### `--min-node-cov`
-Minimum coverage for all nodes in the graph. Default is 1
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-### `--min-cov-ratio`
-Minimum node by window coverage for all nodes. Default is 0.01
-Node to window coverage ratio?
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-### `--max-window-cov`
-Maximum average window coverage before downsampling. Default is 1000
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-### `--min-as-xs-diff`
-Minimum difference between AS and XS scores (BWA-mem). Default is 5
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-### STR Parameters
-Use these flags to deal with Short Tandem Repeats
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-### `--max-str-unit-len`
-Maximum unit length for an STR motif. Default is 4
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-### `--min-str-units`
-Minimum number of STR units required to report. Default is 7
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-### `--maxSTRDist`
-Maximum distance (in bp) of variant from the STR motif. Default is 1
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-### Filters
-These options let you apply different filters to apply to the variant caller
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-### `-c`, `--max-nml-alt-cnt`
-Maximum ALT allele count in normal sample. Default is set at 0
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-### `-C`, `--min-tmr-alt-cnt`
-Minimum ALT allele count in tumor sample. Default is 3
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-### `-v`, `--max-nml-vaf`
-Maximum variant allele frequency in normal sample. Default is 0
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-### `-V`, `--min-tmr-vaf`
-Minimum variant allele frequency in tumor sample. Default is 0.01
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-### `--min-nml-cov`
-Minimum variant coverage in the normal sample. Default is 10
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-### `--min-tmr-cov`
-Minimum variant coverage in the tumor sample. Default is 4
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-### `--max-nml-cov`
-Maximum variant coverage in the normal sample. Default is 1000
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-### `--max-tmr-cov`
-Maximum variant coverage in the tumor sample. Default is 1000
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-### `--min-fisher`
-Minimum phred scaled score for somatic variants. Default is 5
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-### `--min-str-fisher`
-Minimum phred scaled score for STR variants. Default is 25
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-### `--min-strand-cnt`
-Minimum per strand contribution for a variant. Default is 1
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-### Feature Flags
-Use these flags to toggle certain portions of the code to apply different features. By default, these features are off, but by using tags (with no argument following), you can toggle the feature on.
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-### `--verbose`
-Turn on verbose logging for more detailed messages
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-### `--tenx-mode`
-Run Lnacet in 10X Linked Reads mode
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-### `--active-region-off`
-Turn off active region detection
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-### `--kmer-recovery-on`
-Turn on experimental kmer recovery
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-### `--xa-filter`
-Skip reads with XA tag (BWA-mem only)
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-### `--skip-secondary`
-Skip secondary read alignments
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-### `--extract-pairs`
-Extract read pairs for each window
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-### `--no-contig-check`
-Skip checking for same contigs in BAM/CRAMs and reference