Updating files for new release

justincbagley · Dec 17, 2020 · e361d53 · e361d53
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diff --git a/CITATION.md b/CITATION.md
@@ -4,7 +4,7 @@
 
 If you use scripts from this repository as part of your published research, please cite the repository as follows (also see DOI information below): 
 
--   Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.
+-   Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.
 
 Alternatively, provide the following link to this software repository in your manuscript:
 
@@ -14,7 +14,7 @@ Alternatively, provide the following link to this software repository in your ma
 
 The DOI for PIrANHA, via [Zenodo](https://zenodo.org) (also indexed by [OpenAIRE](https://explore.openaire.eu/)), is as follows:  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.596766.svg)](https://doi.org/10.5281/zenodo.596766). Here are some examples of citing PIrANHA using the DOI: 
 
-  Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub package, Available at: http://doi.org/10.5281/zenodo.596766.
+  Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub package, Available at: http://doi.org/10.5281/zenodo.596766.
 
   Bagley, J.C. 2020. PIrANHA. Zenodo, Available at: http://doi.org/10.5281/zenodo.596766.  
 
@@ -50,4 +50,4 @@ BibTeX entries for LaTeX users are as follows:
 ``` 
 
 Justin C. Bagley, Ph.D.
-May 27, 2020, St. Louis, MO
+December 17, 2020, Jacksonville, AL
diff --git a/CODE_OF_CONDUCT.md → CODE-OF-CONDUCT.md b/CODE_OF_CONDUCT.md → CODE-OF-CONDUCT.md
diff --git a/Quick_Guide.md → Quick-Guide.md b/Quick_Guide.md → Quick-Guide.md
@@ -228,13 +228,13 @@ Questions? Comments? Concerns? Bug fix requests? Feature requests for existing f
 
 ### License
 
-All code within **PIrANHA v0.4a3** repository is available "AS IS" under a 3-Clause BSD license. See the [LICENSE](LICENSE) file for more information.
+All code within **PIrANHA v0.4a4** repository is available "AS IS" under a 3-Clause BSD license. See the [LICENSE](LICENSE) file for more information.
 
 ### Citation
 
 If you use scripts from this repository as part of your published research, please cite the repository as follows (also see DOI information below): 
 
--   Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.
+-   Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.
 
 Alternatively, provide the following link to this software repository in your manuscript:
 
@@ -244,7 +244,7 @@ Alternatively, provide the following link to this software repository in your ma
 
 The DOI for PIrANHA, via [Zenodo](https://zenodo.org) (also indexed by [OpenAIRE](https://explore.openaire.eu/)), is as follows:  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.596766.svg)](https://doi.org/10.5281/zenodo.596766). Here are some examples of citing PIrANHA using the DOI: 
 
-  Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub package, Available at: http://doi.org/10.5281/zenodo.596766.
+  Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub package, Available at: http://doi.org/10.5281/zenodo.596766.
 
   Bagley, J.C. 2020. PIrANHA. Zenodo, Available at: http://doi.org/10.5281/zenodo.596766.  
 
@@ -259,6 +259,6 @@ if [[ -f /usr/local/bin/local_piranha ]]; then rm -rf /usr/local/bin/local_piran
 if [[ -f /usr/local/bin/brew_piranha ]]; then rm -rf /usr/local/bin/brew_piranha ; fi
 ```
 
-*December 14, 2020* - *Justin C. Bagley, Jacksonville, AL, USA*
+*December 17, 2020* - *Justin C. Bagley, Jacksonville, AL, USA*
 
 [Next (Introduction) >>](https://github.com/justincbagley/piranha/wiki/1.-Introduction)
diff --git a/Quick-Guide.pdf b/Quick-Guide.pdf
diff --git a/Quick_Guide.pdf b/Quick_Guide.pdf
diff --git a/README.md b/README.md
@@ -34,15 +34,15 @@ For additional information on this distribution, including overview, dependencie
 
 ## LICENSE
 
-All code within **PIrANHA v0.4a3** repository is available "AS IS" under a 3-Clause BSD license. See the [LICENSE](LICENSE) file for more information.
+All code within **PIrANHA v0.4a4** repository is available "AS IS" under a 3-Clause BSD license. See the [LICENSE](LICENSE) file for more information.
 
 ## CITATION
 
 Should you cite **PIrANHA**? See https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md.
 
 If you use scripts from this repository as part of your published research, please cite the repository as follows (also see DOI information below): 
 
--   Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.
+-   Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub repository, Available at: http://github.com/justincbagley/PIrANHA.
 
 Alternatively, provide the following link to this software repository in your manuscript:
 
@@ -52,7 +52,7 @@ Alternatively, provide the following link to this software repository in your ma
 
 The DOI for PIrANHA, via [Zenodo](https://zenodo.org) (also indexed by [OpenAIRE](https://explore.openaire.eu/)), is as follows:  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.596766.svg)](https://doi.org/10.5281/zenodo.596766). Here are some examples of citing PIrANHA using the DOI: 
 
-  Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub package, Available at: http://doi.org/10.5281/zenodo.596766.
+  Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub package, Available at: http://doi.org/10.5281/zenodo.596766.
 
   Bagley, J.C. 2020. PIrANHA. Zenodo, Available at: http://doi.org/10.5281/zenodo.596766.  
 

diff --git a/changeLog.md b/changeLog.md
@@ -10,7 +10,7 @@
 
 Development is on-going...
 
-### PIrANHA 0.4a4 (official minor pre-release version v0.4-alpha-4), December 17, 2020
+### PIrANHA v0.4a4 (official minor pre-release version v0.4-alpha-4), December 17, 2020
 
 -   **December 15, 2020:** Bug fixes for bad piping and other minor errors in `batchRunFolders` and `FASTAsummary` functions, and added option for specifying number of threads when running `batchRunFolders`.
 -   **December 15, 2020:** Fixed version printing for piranha main script and functions (`piranha -V`, `piranha --version`, `piranha -f <function> -V`, and `piranha -f <function> --version` each now yield expected behavior (terse output).
@@ -23,15 +23,15 @@ Development is on-going...
 -   **August 12, 2020:** Updated `trimSeqs` function to improve performance after issue discussion with Juan Moreira. This updated fixed posix space bug, because `[:space:]` should be `[[:space:]]`.
 -   **August 3, 2020:** Updated README, as well as Quick Guide for [wiki](https://github.com/justincbagley/piranha/wiki).
 
-### PIrANHA 0.4a3 (official minor pre-release version v0.4-alpha-3), July 31, 2020
+### PIrANHA v0.4a3 (official minor pre-release version v0.4-alpha-3), July 31, 2020
 
 -   **July 31, 2020:** Added new `trimSeqs` function and prepped 0.4a3 release by updating versioning of main `piranha` script and function scipts, and also updating Wiki and READMEs. The `trimSeqs` function automates trimming one or multiple DNA sequence alignments in PHYLIP format, with options for custom gap handling parameters for trimAl, and with trimmed alignments output to FASTA, PHYLIP, or NEXUS formats.
 -   **May 27, 2020:** Updated repo with new citation file ('CITATION.md'), code of conduct for developers ('CODE_OF_CONDUCT.md'), and license ('LICENSE').
 -   **May 3-5, 2020:** Added new functions. The new `geneCounter` function counts and summarizes number of gene copies per tip taxon label in a set of input gene trees in Newick format, given a taxon-species assignment file (this function written to handle output from HybPiper pipeline; see Usage text). Also added a new `batchRunFolders` function to help setting up input files for batch analyses in several popular software programs for phylogenetics.
 -   **April 18-20, 2020:** This update builds on the previous pre-release, v0.4a2, by adding minor bug fixes and improvements to several functions. With the addition of the new function `alignAlleles`, a companion script meant to be run directly after `phaseAlleles`, this release establishes a new workflow for phasing and aligning consensus sequences from HTS (e.g. targeted sequence capture data) based on reads (re)mapped to a reference assembly FASTA file (i.e. following reference-based assembly). This combination of programs was designed to be run on target capture data after first conducting cleaning, assembly, locus selection, and reference-based assembly (specifically, with SECAPR (Andermann et al. 2018) in mind, and with testing based on output from SECAPR).
 -   **April 17, 2020:** Added "Quick Guide" to wiki, entitled "Quick Guide for the Impatient," with install instructions and example code.
 
-### PIrANHA 0.4a2 (official minor pre-release version v0.4\-alpha\-2), April 17, 2020
+### PIrANHA v0.4a2 (official minor pre-release version v0.4\-alpha\-2), April 17, 2020
 
 -   **April 13-17, 2020:** This update builds on the previous pre-release, v0.4a, by updating the main `prianha` script (including improvements to messaging and help text); addition of a new `phaseAlleles` function that automates phasing of consensus sequences from HTS (e.g. targeted sequence capture) based on a (re)mapped assembly reference FASTA; as well as minor updates to all functions (improved messaging and minor bug fixes).
 

diff --git a/index.html b/index.html
@@ -168,12 +168,12 @@
 
 
       <h2 id="license">LICENSE</h2>
-      <p>All code within the <code class="highlighter-rouge">PIrANHA</code> v0.4a3 repository is available “AS IS” under a 3-Clause BSD license. See the <a href="/PIrANHA/LICENSE">LICENSE</a> file for more information.</p>
+      <p>All code within the <code class="highlighter-rouge">PIrANHA</code> v0.4a4 repository is available “AS IS” under a 3-Clause BSD license. See the <a href="/PIrANHA/LICENSE">LICENSE</a> file for more information.</p>
 
       <h2 id="citation">CITATION</h2>
       <p>If you use scripts from this repository as part of your published research, I require that you cite the repository as follows (also see DOI information below):</p>
       <ul>
-        <li>Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub repository, Available at: <a href="https://github.com/justincbagley/piranha">http://github.com/justincbagley/PIrANHA</a>.</li>
+        <li>Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub repository, Available at: <a href="https://github.com/justincbagley/piranha">http://github.com/justincbagley/PIrANHA</a>.</li>
       </ul>
 
       <p>Alternatively, please provide the following link to this software repository in your manuscript:</p>
@@ -183,7 +183,7 @@ <h2 id="citation">CITATION</h2>
 
  <h2 id="doi">DOI</h2>
       <p>The DOI for <code class="highlighter-rouge">PIrANHA</code>, via <a href="https://zenodo.org">Zenodo</a>, is as follows:  <a href="https://doi.org/10.5281/zenodo.596766"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.596766.svg" alt="DOI" /></a>. Here are some examples of citing PIrANHA using the DOI:</p>
-      <p>Bagley, J.C. 2020. PIrANHA v0.4a3. GitHub package, Available at: <a href="http://doi.org/10.5281/zenodo.596766">http://doi.org/10.5281/zenodo.596766</a>.</p>
+      <p>Bagley, J.C. 2020. PIrANHA v0.4a4. GitHub package, Available at: <a href="http://doi.org/10.5281/zenodo.596766">http://doi.org/10.5281/zenodo.596766</a>.</p>
       <p>Bagley, J.C. 2020. PIrANHA. Zenodo, Available at: <a href="http://doi.org/10.5281/zenodo.596766">http://doi.org/10.5281/zenodo.596766</a>.</p>
 
 <h2 id="documentation">DOCUMENTATION</h2>