From af691b46e7cc1e0df6fed2c2ca3aaf7c3e04b284 Mon Sep 17 00:00:00 2001
From: Xian <xhchang@ucsc.edu>
Date: Thu, 28 Nov 2024 16:05:42 +0100
Subject: [PATCH] Trim down man page

---
 doc/man.md          | 24 ++++++++++++++----------
 doc/vgmanmd.desc.md | 10 ----------
 doc/vgmanmd.py      |  2 +-
 3 files changed, 15 insertions(+), 21 deletions(-)

diff --git a/doc/man.md b/doc/man.md
index e4a87c88ca..d97aa2b4c2 100644
--- a/doc/man.md
+++ b/doc/man.md
@@ -351,16 +351,6 @@ options:
 
 Filter alignments by properties.
 
-`vg filter --tsv-out` can be used to produce a TSV file of user-specified fields from the GAM file. For example, 
-
-`vg filter --tsv-out "name;mapping_quality" <alignment.gam>`
-
-is the equivalent of 
-
-`vg view -aj <alignment.gam> | jq -r '[.name,.mapping_quality] | @tsv'`
-
-To find which fields are stored in a GAM file, use [`vg view`](#view) to view the GAM as a JSON file. 
-
 
 
 
@@ -798,6 +788,20 @@ snarl distance index options
 ```
 
 
+## inject
+
+
+```
+usage: vg inject -x graph.xg [options] input.[bam|sam|cram] >output.gam
+
+options:
+    -x, --xg-name FILE       use this graph or xg index (required, non-XG formats also accepted)
+    -o, --output-format NAME output the alignments in NAME format (gam / gaf / json) [gam]
+    -t, --threads N          number of threads to use
+
+```
+
+
 ## map
 
 
diff --git a/doc/vgmanmd.desc.md b/doc/vgmanmd.desc.md
index 7bb6227a16..3b769e9cf8 100644
--- a/doc/vgmanmd.desc.md
+++ b/doc/vgmanmd.desc.md
@@ -90,13 +90,3 @@ format conversions for graphs and alignments
 # filter
 
 Filter alignments by properties.
-
-`vg filter --tsv-out` can be used to produce a TSV file of user-specified fields from the GAM file. For example, 
-
-`vg filter --tsv-out "name;mapping_quality" <alignment.gam>`
-
-is the equivalent of 
-
-`vg view -aj <alignment.gam> | jq -r '[.name,.mapping_quality] | @tsv'`
-
-To find which fields are stored in a GAM file, use [`vg view`](#view) to view the GAM as a JSON file. 
diff --git a/doc/vgmanmd.py b/doc/vgmanmd.py
index 984994e26e..833aa1b6a0 100644
--- a/doc/vgmanmd.py
+++ b/doc/vgmanmd.py
@@ -6,7 +6,7 @@
 cmds = ['index', 'view', 'autoindex', 'pack', 'giraffe', 'map', 'call',
         'mpmap', 'rna', 'chunk', 'stats', 'gbwt', 'paths', 'find', 'filter',
         'construct', 'minimizer', 'haplotypes', 'deconstruct', 'convert',
-        'gamsort', 'surject', 'mod', 'prune', 'ids', 'sim', 'annotate']
+        'gamsort', 'inject', 'surject', 'mod', 'prune', 'ids', 'sim', 'annotate']
 cmds.sort()
 
 # parse short descriptions