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EBIvariation / vcf-validator

Validation suite for Variant Call Format (VCF) files, implemented using C++11
Apache License 2.0
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Add Assembly_report Library #171

Closed srbcheema1 closed 5 years ago

srbcheema1 commented 5 years ago

This PR is to add a new library assembly_report which will have functionality to map contigs to their synonyms list.

srbcheema1 commented 5 years ago

@cyenyxe @jmmut I have added the mapping functionality in assembly_checker.

you may check it by running it as 

$ cd test/input_files/v4.3/assembly_checker/passed/passed_with_mapping/
$ ./vcf_assembly_checker -i passed_with_mapping.vcf -f passed_with_mapping.fa 
[info] Reading from input FASTA file...
[info] Reading from input FASTA index file...
[info] Reading from input VCF file...
[info] Number of matches: 0/0
[info] Percentage of matches: -nan%
$ ./vcf_assembly_checker -i passed_with_mapping.vcf -f passed_with_mapping.fa -a assembly_report.txt
[info] Reading from input FASTA file...
[info] Reading from input FASTA index file...
[info] Reading from input VCF file...
[info] Number of matches: 247/247
[info] Percentage of matches: 100%
jmmut commented 5 years ago

the code looks fine but I want to give it a try manually before merging