Rename noise-profile plugin

The new (and more appropriate) name is afs, which stands for Allelic Frequency Score

NEWS

@@ -7,10 +7,10 @@ Changes affecting the whole of bcftools, or multiple commands:
 
 Changes affecting specific commands:
 
-* bcftools +noise-profile
+* bcftools +afs
 
-    - New experimental plugin for scoring variants and assess site noisiness from a large number of unaffected
-      parental samples
+    - New experimental plugin for scoring variants and assess site noisiness (allelic frequency profiles)
+      from a large number of unaffected parental samples
 
 * bcftools query
 

doc/bcftools.txt

@@ -2848,6 +2848,9 @@ By default, appropriate system directories are searched for installed plugins.
 *af-dist*::
     collect AF deviation stats and GT probability distribution given AF and assuming HWE
 
+*afs*::
+    assess site noisiness (allelic frequency score) from a large number of unaffected parental samples
+
 *allele-length*::
     count the frequency of the length of REF, ALT and REF+ALT
 
@@ -2939,9 +2942,6 @@ By default, appropriate system directories are searched for installed plugins.
 *missing2ref*::
     sets missing genotypes ("./.") to ref allele ("0/0" or "0|0")
 
-*noise-profile*::
-    assess site noisiness from a large number of unaffected parental samples
-
 *parental-origin*::
     determine parental origin of a CNV region
 

plugins/noise-profile.c → plugins/afs.c

@@ -91,14 +91,14 @@ args_t;
 
 const char *about(void)
 {
-    return "Localised assessment of sequencing artefacts, estimate site noisiness\n";
+    return "Localised assessment of sequencing artefacts, estimate site noisiness (allelic frequency score)\n";
 }
 static const char *usage_text(void)
 {
     return
         "\n"
-        "About: Assess site noisiness from a large number of unaffected parental samples\n"
-        "Usage: bcftools +noise-profile [OPTIONS]\n"
+        "About: Assess site noisiness (allelic frequency score) from a large number of unaffected parental samples\n"
+        "Usage: bcftools +afs [OPTIONS]\n"
         "\n"
         "Required options:\n"
         "   -a, --alns FILE               List of BAM/CRAM files\n"
@@ -124,16 +124,16 @@ static const char *usage_text(void)
         "\n"
         "Example:\n"
         "   # Typical run\n"
-        "   bcftools +noise-profile -f ref.fa -a bams.txt -s sites.txt -o scores.txt\n"
+        "   bcftools +afs -f ref.fa -a bams.txt -s sites.txt -o scores.txt\n"
         "\n"
         "   # Run in batches. Let's say one batch can have at most 3 bams and there are 5 bams in total\n"
         "   #   1) find out the number of required batches with `--batch k=3` (the program outputs: 2)\n"
         "   #   2) run all batches individually with `--batch 1/2` and `--batch 2/2`\n"
         "   #   3) create a list of outputs and merge with `--merge-batches list.txt`\n"
-        "   bcftools +noise-profile -a bams.txt --batch k=3     # prints 2\n"
-        "   bcftools +noise-profile -f ref.fa -a bams.txt -s sites.txt -o scores1.txt --batch 1/2\n"
-        "   bcftools +noise-profile -f ref.fa -a bams.txt -s sites.txt -o scores2.txt --batch 2/2\n"
-        "   bcftools +noise-profile --merge-batches list.txt\n"
+        "   bcftools +afs -a bams.txt --batch k=3     # prints 2\n"
+        "   bcftools +afs -f ref.fa -a bams.txt -s sites.txt -o scores1.txt --batch 1/2\n"
+        "   bcftools +afs -f ref.fa -a bams.txt -s sites.txt -o scores2.txt --batch 2/2\n"
+        "   bcftools +afs --merge-batches list.txt\n"
         "\n";
 }
 

plugins/noise-profile.mk → plugins/afs.mk

@@ -1,2 +1,2 @@
-plugins/noise-profile.so: plugins/noise-profile.c version.h regidx.h mpileup2/mpileup.o
+plugins/afs.so: plugins/afs.c version.h regidx.h mpileup2/mpileup.o
 	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(PLUGIN_LIBS) $(LIBS)