Merge pull request #126 from paulsengroup/docs/update

Update docs
paulsengroup · Feb 25, 2024 · e43ae50 · e43ae50
2 parents 698452c + 55af86c
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Showing 2 changed files with 20 additions and 6 deletions.
diff --git a/docs/cli_reference.rst b/docs/cli_reference.rst
@@ -116,6 +116,9 @@ hictk convert
     -l,--compression-lvl UINT:INT in [1 - 12] [6]
                                 Compression level used to compress interactions.
                                 Defaults to 6 and 10 for .cool and .hic files, respectively.
+    --skip-all-vs-all,--no-skip-all-vs-all{false}
+                                Do not generate All vs All matrix.
+                                Has no effect when creating .[m]cool files.
     -f,--force                  Overwrite existing files (if any).
 
 hictk dump
@@ -252,6 +255,9 @@ hictk merge
                                 Maximum number of parallel threads to spawn.
                                 When merging interactions in Cooler format, only a single thread will be used.
     --tmpdir TEXT [/tmp]        Path to a folder where to store temporary data.
+    --skip-all-vs-all,--no-skip-all-vs-all{false}
+                                Do not generate All vs All matrix.
+                                Has no effect when merging .cool files.
     -v,--verbosity UINT:INT in [1 - 4] []
                                 Set verbosity of output to the console.
 
@@ -323,6 +329,9 @@ hictk zoomify
     --chunk-size UINT [10000000]
                                 Number of pixels to buffer in memory.
                                 Only used when zoomifying .hic files.
+    --skip-all-vs-all,--no-skip-all-vs-all{false}
+                                Do not generate All vs All matrix.
+                                Has no effect when zoomifying .cool files.
     --tmpdir TEXT [/tmp]        Path to a folder where to store temporary data.
     -v,--verbosity UINT:INT in [1 - 4] []
                                 Set verbosity of output to the console.
diff --git a/docs/index.rst b/docs/index.rst
@@ -45,12 +45,17 @@ discourse:
 
 .. code-block:: bibtex
 
-    @misc{hictk,
-       author = {Roberto Rossini},
-       year = {2023},
-       note = {https://github.com/paulsengroup/hictk},
-       title = {hictk: blazing fast toolkit to work with .hic and .cool files}
-    }
+  @article {hictk,
+	  author = {Roberto Rossini and Jonas Paulsen},
+	  title = {hictk: blazing fast toolkit to work with .hic and .cool files},
+	  elocation-id = {2023.11.26.568707},
+	  year = {2023},
+	  doi = {10.1101/2023.11.26.568707},
+	  publisher = {Cold Spring Harbor Laboratory},
+	  URL = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707},
+	  eprint = {https://www.biorxiv.org/content/early/2023/11/27/2023.11.26.568707.full.pdf},
+	  journal = {bioRxiv}
+  }
 
 If you use ``hictk convert`` to convert .[m]cool files to .hic format you should also cite JuicerTools or HiCTools.