Clarified assembly checker section in README file
@@ -52,7 +52,7 @@ Each report is written into its own file and it is named after the input file, f
### Debugulator
-There are some simple errors that can be automatically fixed. The most common error is the presence of duplicate variants. The needed parameters are the original VCF and the report generated by a previous run of the vcf_validator with the option `-r database`.
+There are some simple errors that can be automatically fixed. The most common error is the presence of duplicate variants. The needed parameters are the original VCF and the report generated by a previous run of the validator with the option `-r database`.
The fixed VCF will be written into the standard output, which you can redirect to a file, or use the `-o` / `--output` option and specify the desired file name.
@@ -60,7 +60,9 @@ The logs about what the debugulator is doing will be written into the error outp
### Assembly Checker
-Assembly Checker is a tool to check the validity of a VCF file with respect to the fasta file. Assembly Checker reads the CHR, POS and REF columns in the VCF, and for each line, look into the FASTA file to see if the REF sequence matches in that region. A VCF file is said to be valid if all the variants matches with the sequence in fasta file. Assembly Checker requires a fasta-index file with extension `.fai` for indexed reading of fasta file.
+vcf-assembly-checker assesses the correctness of a VCF file with respect to a FASTA file (that should contain the reference sequence). The assembly checker reads the CHR, POS and REF columns from the VCF, and for each line, looks into the FASTA file to see if the REF allele matches that region. A VCF file is considered valid if all the variants match the sequence in the FASTA file.
+
+vcf-assembly-checker requires a FASTA-index file with extension `.fai` for efficient reading of the FASTA file.
Different types of validation reports can be written with the `-r` / `--report` option. Several ones may be specified in the same execution, using commas to separate each type (without spaces, e.g.: `-r summary,valid,text`).
@@ -234,9 +236,9 @@ In order to run those binaries, you will need to add the `lib/windows_specific`
The following binaries are be created after successful build:
-* `vcf_validator`: validation tool
-* `vcf_debugulator`: automatic fixing tool
-* `vcf_assembly_checker`: variant checking tool
+* `vcf_validator`: VCF validation tool
+* `vcf_debugulator`: automatic VCF fixing tool
+* `vcf_assembly_checker`: variant checking tool against FASTA sequence
* `test_validation_suite` and derivatives: testing correct behaviour of the tools listed above
