adding -c parameter to docs for consensus

andersen-lab · Feb 25, 2023 · c1eced4 · c1eced4
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diff --git a/docs/MANUAL.md b/docs/MANUAL.md
@@ -288,6 +288,7 @@ Note : samtools mpileup output must be piped into ivar consensus
 Input Options    Description
            -q    Minimum quality score threshold to count base (Default: 20)
            -t    Minimum frequency threshold(0 - 1) to call consensus. (Default: 0)
+           -c    Minimum insertion frequency threshold(0 - 1) to call consensus. (Default: 0.8)
                  Frequently used thresholds | Description
                  ---------------------------|------------
                                           0 | Majority or most common base

diff --git a/docs/html/manualpage.html b/docs/html/manualpage.html
@@ -352,6 +352,7 @@ <h2><a class="anchor" id="autotoc_md19"></a>
 <div class="line">Input Options    Description</div>
 <div class="line">           -q    Minimum quality score threshold to count base (Default: 20)</div>
 <div class="line">           -t    Minimum frequency threshold(0 - 1) to call consensus. (Default: 0)</div>
+<div class="line">           -c    Minimum insertion frequency threshold(0 - 1) to call consensus. (Default: 0.8)</div>
 <div class="line">                 Frequently used thresholds | Description</div>
 <div class="line">                 ---------------------------|------------</div>
 <div class="line">                                          0 | Majority or most common base</div>

diff --git a/docs/latex/manualpage.tex b/docs/latex/manualpage.tex
@@ -348,6 +348,7 @@
 \DoxyCodeLine{Input Options    Description}
 \DoxyCodeLine{           -\/q    Minimum quality score threshold to count base (Default: 20)}
 \DoxyCodeLine{           -\/t    Minimum frequency threshold(0 -\/ 1) to call consensus. (Default: 0)}
+\DoxyCodeLine{           -\/c    Minimum insertion frequency threshold(0 -\/ 1) to call consensus. (Default: 0.8)}
 \DoxyCodeLine{                 Frequently used thresholds | Description}
 \DoxyCodeLine{                 -\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/|-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/-\/}
 \DoxyCodeLine{                                          0 | Majority or most common base}

diff --git a/docs/man/man3/manualpage.3 b/docs/man/man3/manualpage.3
@@ -247,6 +247,7 @@ Note : samtools mpileup output must be piped into ivar consensus
 Input Options    Description
            -q    Minimum quality score threshold to count base (Default: 20)
            -t    Minimum frequency threshold(0 - 1) to call consensus\&. (Default: 0)
+           -c    Minimum insertion frequency threshold(0 - 1) to call consensus\&. (Default: 0\&.8)
                  Frequently used thresholds | Description
                  ---------------------------|------------
                                           0 | Majority or most common base