feat: Updated simgenotype to allow only breakpoint generation (#167)

Co-authored-by: Arya Massarat <[email protected]>
CAST-genomics · Jan 28, 2023 · c0c3c97 · c0c3c97
1 parent 6995407
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diff --git a/docs/commands/simgenotype.rst b/docs/commands/simgenotype.rst
@@ -38,6 +38,7 @@ Parameter Descriptions
 * ``--pop_field`` - Flag for ouputting population field in VCF output. Note this flag does not work when your output is in PGEN format. [Optional]
 * ``--sample_field`` - Flag for ouputting sample field in VCF output. Note this flag does not work when your output is in PGEN format. Should only be used for debugging. [Optional]
 * ``--verbosity`` - What level of output the logger should print to stdout. Please see `logging levels <https://docs.python.org/3/library/logging.html>`_ for output levels. Default = INFO [Optional]
+* ``--only_breakpoint`` - Flag which when provided only outputs the breakpoint file. Note you will not need to provide a ``--ref_vcf`` or ``--sample_info`` file and can instead put NA. eg.  ``--ref_vcf NA`` and ``--sample_info NA`` [Optional]
 
 File Formats
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diff --git a/haptools/__main__.py b/haptools/__main__.py
@@ -181,7 +181,6 @@ def karyogram(bp, sample, out, title, centromeres, colors, verbosity):
 )
 @click.option(
     "--only_breakpoint",
-    hidden=True,
     is_flag=True,
     required=False,
     help=(