Note -print-metrics argument is deprecated.

bigdatagenomics · Mar 2, 2020 · f849aa1 · f849aa1
1 parent 7378924
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Showing 4 changed files with 12 additions and 6 deletions.
diff --git a/docs/cli/actions.rst b/docs/cli/actions.rst
@@ -344,7 +344,8 @@ This command takes several optional arguments:
 
 This command does not support Parquet output, so the only `default
 options <#default-args>`__ that this command supports is
-``-print_metrics``.
+``-print_metrics``. Note ``-print_metrics`` is deprecated in ADAM version
+0.31.0 and will be removed in version 0.32.0.
 
 coverage
 ~~~~~~~~~~~~~~

diff --git a/docs/cli/conversions.rst b/docs/cli/conversions.rst
@@ -19,8 +19,10 @@ optional third argument:
    the second-of-pair reads to.
 
 ``adam2fastq`` only supports the ``-print_metrics`` option from the
-`default options <#default-args>`__. Additionally, ``adam2fastq`` takes
-the following options:
+`default options <#default-args>`__. Note ``-print_metrics`` is deprecated
+in ADAM version 0.31.0 and will be removed in version 0.32.0.
+
+Additionally, ``adam2fastq`` takes the following options:
 
 -  ``-no_projection``: By default, ``adam2fastq`` only projects the
    fields necessary for saving to FASTQ. This option disables that

diff --git a/docs/cli/overview.rst b/docs/cli/overview.rst
@@ -51,7 +51,8 @@ commands. These include:
    Parquet files. Defaults to 1MB (1024 \* 1024).
 -  ``-print_metrics``: If provided, prints the
    `instrumentation <https://github.com/bigdatagenomics/utils#instrumentation>`__
-   metrics to the log when the CLI operation terminates.
+   metrics to the log when the CLI operation terminates. Note ``-print_metrics`` is
+   deprecated in ADAM version 0.31.0 and will be removed in version 0.32.0.
 
 Legacy output options
 ---------------------

diff --git a/docs/cli/printers.rst b/docs/cli/printers.rst
@@ -21,7 +21,8 @@ This command has several options:
 
 This command does not support Parquet output, so the only `default
 options <#default-args>`__ that this command supports is
-``-print_metrics``.
+``-print_metrics``. Note ``-print_metrics`` is deprecated in ADAM version
+0.31.0 and will be removed in version 0.32.0.
 
 flagstat
 ~~~~~~~~
@@ -43,7 +44,8 @@ This command has several options:
 
 This command does not support Parquet output, so the only `default
 options <#default-args>`__ that this command supports is
-``-print_metrics``.
+``-print_metrics``. Note ``-print_metrics`` is deprecated in ADAM version
+0.31.0 and will be removed in version 0.32.0.
 
 view
 ~~~~