From 1b4de339a7efb47c0026ec15bd03f00ca2242174 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 8 Nov 2022 13:56:16 -0800 Subject: [PATCH] distance: Fix/normalize end-of-sentence punctuation --- docs/usage/cli/distance.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/usage/cli/distance.rst b/docs/usage/cli/distance.rst index 63e512a65..84c9ad0c8 100644 --- a/docs/usage/cli/distance.rst +++ b/docs/usage/cli/distance.rst @@ -52,7 +52,7 @@ Distance maps are defined in JSON format with two required top-level keys. The `default` key specifies the numeric (floating point) value to assign to all mismatches by default. The `map` key specifies a dictionary of weights to use for distance calculations. These weights are indexed hierarchically by gene name and one-based gene coordinate and are assigned in either a sequence-independent or sequence-dependent manner. -The simplest possible distance map calculates Hamming distance between sequences without any site-specific weights, as shown below:: +The simplest possible distance map calculates Hamming distance between sequences without any site-specific weights, as shown below: .. code-block:: json @@ -63,7 +63,7 @@ The simplest possible distance map calculates Hamming distance between sequences } By default, distances are floating point values whose precision can be controlled with the `precision` key that defines the number of decimal places to retain for each distance. -The following example shows how to specify a precision of two decimal places in the final output.:: +The following example shows how to specify a precision of two decimal places in the final output: .. code-block:: json @@ -74,7 +74,7 @@ The following example shows how to specify a precision of two decimal places in "precision": 2 } -Distances can be reported as integer values by specifying an `output_type` as `integer` or `int` as follows.:: +Distances can be reported as integer values by specifying an `output_type` as `integer` or `int` as follows: .. code-block:: json @@ -89,7 +89,7 @@ Sequence-independent distances are defined by gene and position using a numeric value of the same type as the default value (integer or float). The following example is a distance map for antigenic amino acid substitutions near influenza A/H3N2 HA's receptor binding sites. This map calculates the Hamming distance -between amino acid sequences only at seven positions in the HA1 gene:: +between amino acid sequences only at seven positions in the HA1 gene: .. code-block:: json @@ -113,7 +113,7 @@ Sequence-dependent distances are defined by gene, position, and sequence pairs where the `from` sequence in each pair is interpreted as the ancestral state and the `to` sequence as the derived state. The following example is a distance map that assigns asymmetric weights to specific amino acid substitutions at a -specific position in the influenza gene HA1:: +specific position in the influenza gene HA1: .. code-block:: json @@ -142,7 +142,7 @@ that can be passed to `augur export`. In addition to the standard `nodes` field, the JSON includes a `params` field that describes the mapping of attribute names to requested comparisons and distance maps and any date parameters specified by the user. The following example JSON shows a sample output when the distance -command is run with multiple comparisons and distance maps:: +command is run with multiple comparisons and distance maps: .. code-block:: json