VcfParser.java currently calls Pattern.split per line, which is quite expensive for larger files.
Can I send a pull request to replace the four Pattern splitters with Google's Guava Splitter to speed up parsing? It's twice as fast on a 700k line VCF file and passes all of PharmCat's tests.
Note: Guava preserves trailing delimiters. While this wouldn't happen in a regular .vcf file, if a line had a trailing delimiter the code would need extra checks.
VcfParser.java currently calls Pattern.split per line, which is quite expensive for larger files.
Can I send a pull request to replace the four Pattern splitters with Google's Guava Splitter to speed up parsing? It's twice as fast on a 700k line VCF file and passes all of PharmCat's tests.
Note: Guava preserves trailing delimiters. While this wouldn't happen in a regular .vcf file, if a line had a trailing delimiter the code would need extra checks.