updates test files for --help

CGATOxford · Mar 6, 2024 · 636381c · 636381c
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commit 636381c
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Showing 4 changed files with 34 additions and 28 deletions.
diff --git a/tests/count_help b/tests/count_help
@@ -71,15 +71,6 @@ Options:
     --mapping-quality=MAPPING_QUALITY
                         Minimum mapping quality for a read to be retained
                         [default=0]
-    --unmapped-reads=UNMAPPED_READS
-                        How to handle unmapped reads. Options are 'discard',
-                        'use' or 'correct' [default=discard]
-    --chimeric-pairs=CHIMERIC_PAIRS
-                        How to handle chimeric read pairs. Options are
-                        'discard', 'use' or 'correct' [default=use]
-    --unpaired-reads=UNPAIRED_READS
-                        How to handle unpaired reads. Options are 'discard',
-                        'use' or 'correct' [default=use]
     --ignore-umi        Ignore UMI and dedup only on position
     --ignore-tlen       Option to dedup paired end reads based solely on
                         read1, whether or not the template length is the same
@@ -90,6 +81,17 @@ Options:
     -o, --out-sam       Output alignments in sam format [default=False]
     --no-sort-output    Don't Sort the output
 
+  Dedup and Count SAM/BAM options:
+    --unmapped-reads=UNMAPPED_READS
+                        How to handle unmapped reads. Options are 'discard' or
+                        'use' [default=discard]
+    --chimeric-pairs=CHIMERIC_PAIRS
+                        How to handle chimeric read pairs. Options are
+                        'discard' or 'use'  [default=use]
+    --unpaired-reads=UNPAIRED_READS
+                        How to handle unpaired reads. Options are 'discard'or
+                        'use' [default=use]
+
   input/output options:
     -I FILE, --stdin=FILE
                         file to read stdin from [default = stdin].

diff --git a/tests/dedup_help b/tests/dedup_help
@@ -81,15 +81,6 @@ Options:
     --mapping-quality=MAPPING_QUALITY
                         Minimum mapping quality for a read to be retained
                         [default=0]
-    --unmapped-reads=UNMAPPED_READS
-                        How to handle unmapped reads. Options are 'discard',
-                        'use' or 'correct' [default=discard]
-    --chimeric-pairs=CHIMERIC_PAIRS
-                        How to handle chimeric read pairs. Options are
-                        'discard', 'use' or 'correct' [default=use]
-    --unpaired-reads=UNPAIRED_READS
-                        How to handle unpaired reads. Options are 'discard',
-                        'use' or 'correct' [default=use]
     --ignore-umi        Ignore UMI and dedup only on position
     --ignore-tlen       Option to dedup paired end reads based solely on
                         read1, whether or not the template length is the same
@@ -100,6 +91,17 @@ Options:
     -o, --out-sam       Output alignments in sam format [default=False]
     --no-sort-output    Don't Sort the output
 
+  Dedup and Count SAM/BAM options:
+    --unmapped-reads=UNMAPPED_READS
+                        How to handle unmapped reads. Options are 'discard' or
+                        'use' [default=discard]
+    --chimeric-pairs=CHIMERIC_PAIRS
+                        How to handle chimeric read pairs. Options are
+                        'discard' or 'use'  [default=use]
+    --unpaired-reads=UNPAIRED_READS
+                        How to handle unpaired reads. Options are 'discard'or
+                        'use' [default=use]
+
   input/output options:
     -I FILE, --stdin=FILE
                         file to read stdin from [default = stdin].

diff --git a/tests/group_help b/tests/group_help
@@ -84,15 +84,6 @@ Options:
     --mapping-quality=MAPPING_QUALITY
                         Minimum mapping quality for a read to be retained
                         [default=0]
-    --unmapped-reads=UNMAPPED_READS
-                        How to handle unmapped reads. Options are 'discard',
-                        'use' or 'correct' [default=discard]
-    --chimeric-pairs=CHIMERIC_PAIRS
-                        How to handle chimeric read pairs. Options are
-                        'discard', 'use' or 'correct' [default=use]
-    --unpaired-reads=UNPAIRED_READS
-                        How to handle unpaired reads. Options are 'discard',
-                        'use' or 'correct' [default=use]
     --ignore-umi        Ignore UMI and dedup only on position
     --ignore-tlen       Option to dedup paired end reads based solely on
                         read1, whether or not the template length is the same
@@ -103,6 +94,17 @@ Options:
     -o, --out-sam       Output alignments in sam format [default=False]
     --no-sort-output    Don't Sort the output
 
+  Group SAM/BAM options:
+    --unmapped-reads=UNMAPPED_READS
+                        How to handle unmapped reads. Options are 'discard',
+                        'use' or 'output' [default=discard]
+    --chimeric-pairs=CHIMERIC_PAIRS
+                        How to handle chimeric read pairs. Options are
+                        'discard', 'use' or 'output' [default=use]
+    --unpaired-reads=UNPAIRED_READS
+                        How to handle unpaired reads. Options are 'discard',
+                        'use' or 'output' [default=use]
+
   input/output options:
     -I FILE, --stdin=FILE
                         file to read stdin from [default = stdin].

diff --git a/umi_tools/Utilities.py b/umi_tools/Utilities.py
@@ -928,7 +928,7 @@ def Start(parser=None,
                          choices=("discard", "use"),
                          default="discard",
                          help=("How to handle unmapped reads. Options are "
-                               "'discard' or 'use'' [default=%default]"))
+                               "'discard' or 'use' [default=%default]"))
 
         group.add_option("--chimeric-pairs", dest="chimeric_pairs",
                          type="choice",