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paulsengroup · Dec 4, 2023 · 1c67c55 · 1c67c55
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Showing 2 changed files with 26 additions and 3 deletions.
diff --git a/docs/cli_reference.rst b/docs/cli_reference.rst
@@ -139,12 +139,16 @@ hictk dump
                                 Matrix unit (ignored when file is not in .hic format).
     -t,--table TEXT:{chroms,bins,pixels,normalizations,resolutions,cells} [pixels]
                                 Name of the table to dump.
-    -r,--range TEXT [all]  Excludes: --query-file
+    -r,--range TEXT [all]  Excludes: --query-file --cis-only --trans-only
                                 Coordinates of the genomic regions to be dumped following UCSC-style notation (chr1:0-1000).
-    --range2 TEXT [all]  Needs: --range Excludes: --query-file
+    --range2 TEXT [all]  Needs: --range Excludes: --query-file --cis-only --trans-only
                                 Coordinates of the genomic regions to be dumped following UCSC-style notation (chr1:0-1000).
-    --query-file TEXT:(FILE) OR ({-}) Excludes: --range --range2
+    --query-file TEXT:(FILE) OR ({-}) Excludes: --range --range2 --cis-only --trans-only
                                 Path to a BEDPE file with the list of coordinates to be fetched (pass - to read queries from stdin).
+    --cis-only Excludes: --range --range2 --query-file --trans-only
+                                Dump intra-chromosomal interactions only.
+    --trans-only Excludes: --range --range2 --query-file --cis-only
+                                Dump inter-chromosomal interactions only.
     -b,--balance TEXT [NONE]    Balance interactions using the given method.
     --sorted,--unsorted{false}  Return interactions in ascending order.
     --join,--no-join{false}     Output pixels in BG2 format.

diff --git a/docs/reading_interactions.rst b/docs/reading_interactions.rst
@@ -106,3 +106,22 @@ Dump tables other than pixels:
   5000
   10000
   ...
+
+
+Dump cis or trans interactions only:
+
+.. code-block:: console
+
+  user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --cis-only --join
+
+  chr2L	7000	8000	chr2L	7000	8000	1745
+  chr2L	7000	8000	chr2L	12000	13000	1766
+  chr2L	7000	8000	chr2L	17000	18000	1078
+  ...
+
+  user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1000 --trans-only --join
+
+  chr2L	7000	8000	chr2R	27000	28000	1
+  chr2L	7000	8000	chr2R	322000	323000	1
+  chr2L	7000	8000	chr2R	397000	398000	1
+  ...