Merge branch 'main' of https://github.com/ebioman/AgnosticBamCounter

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name    = "abc"
-version = "0.3.1"
+version = "0.3.3"
 authors = ["Emanuel Schmid-Siegert"]
 description   =  """
 The Agnostic Bam Counter (abc) determines at a given positions the count of observed nucleotides.

README.md

@@ -9,7 +9,7 @@ The Agnostic Bam Counter (abc) determines at a given positions the count of obse
 Simply supply a bed file with positions and obtains a tsv file with counts for each ATCG and reference if provided
 
 ```
-abc 0.3.1
+abc 0.3.2
 Emanuel Schmid-Siegert
 The Agnostic Bam Counter (abc) determines at a given positions the count of observed nucleotides.
 Simply supply a bed file with positions and obtains a tsv file with counts for each ATCG and reference if provided.
@@ -42,26 +42,25 @@ OPTIONS:
 ## Limitations
 
  - the bed-file currently accepts only single nucleotide positions, no ranges.
- - systematic testing missing so far
+ - systematic testing is not complete
 
 ## Output
 
 Example:
 
 ```
-##	abc:	0.2.2											
+##	abc:	0.3.2											
 ##	author:	Emanuel Schmid-Siegert											
-##	date:	Sat, 11 Sep 2021 07:35:03 +0200										
-##	command:	target/release/abc --bam test/test_mpileup.bam --positions test/test_mpileup.bed --outfile test/test_mpileup.out.tsv --reference test/test_ref.fa									
+##	date:	Thu, 03 Aug 2023 06:57:33 +0200										
+##	command:	target/debug/abc --bam test/test_mpileup.bam --positions test/test_mpileup.bed --outfile test/test_mpileup.out.tsv --reference test/test_ref.fa									
 # chromosome	start	end	reference	A	T	C	G	ambigious	ins	del	depthVAF	RAF
-17	301	302	T	1	8	0	0	0	8	0	17	0.5294	0.4706
+21	10405200	10405201	C	0	2	55	0	0	0	0	57	0.03510.9649
+21	10402985	10402986	A	340	1	2	0	0	0	0	343	0.00580.9913
+17	1884	1885	C	0	0	20	0	0	0	0	20	0.0000	1.0000
+17	1870	1871	C	0	0	18	0	0	0	0	18	0.0000	1.0000
+17	1869	1870	C	0	0	18	0	0	0	0	18	0.0000	1.0000
+17	303	304	C	0	0	17	0	0	0	0	17	0.0000	1.0000
 17	302	303	G	0	0	0	17	0	0	0	17	0.0000	1.0000
-17	827	828	T	0	2	11	0	0	0	0	13	0.8462	0.1538
-17	1868	1869	A	11	7	0	0	0	0	0	18	0.3889	0.6111
-17	2040	2041	G	13	0	0	10	0	0	0	23	0.5652	0.4348
-21	10402805	10402806	A	87	0	0	0	0	0	0	87	0.00001.0000
-21	10402975	10402976	C	2	2	333	0	0	0	0	337	0.01190.9881
-
 ```
 
 The header contains the version and author of the program as well as the execution time and the used command.
@@ -79,4 +78,9 @@ We have then in the table the following columns:
  - number of reads with an insertion
  - number of reads with a deletion at that position
  - the depth at that position
- - information if mutated or not (true only possible with reference)
+ - VAF = variant allele frequency
+ - RAF = reference allele frequency
+
+ Important: VAF and RAF are taking ** all ** modifications into account , as well insertion and deletions.
+ It can happen that a VAF reported is actually the insertion or deletion event.
+

changelog.txt

@@ -0,0 +1,6 @@
+# v0.3.3
+- hotfix as del was not correctly counted for depth
+# v0.3.2
+- separate functions into lib
+- simplify analysis of RAF&VAF
+- calculate VAF based on dominant mutation only