VCF 4.3 writing.#1596

Draft

cmnbroad wants to merge 24 commits intomasterfrom

cn_vcf43_writer

Commits on Mar 13, 2023

Commits on Jun 27, 2023

Properly handle info fields with embedded spaces by VCF version.
cmnbroad
committed
Remove unnecessary null test.
cmnbroad
committed
Properly handle info fields with embedded spaces by VCF version.
cmnbroad
committed
Add VCF 4.3 writing

Anders Leung
authored and
cmnbroad
committed
Refactor VariantContext decoding, decode VCs with different version from header on write

Anders Leung
authored and
cmnbroad
committed
Move version upgrading from codec to VCFWriter

Anders Leung
authored and
cmnbroad
committed
Fix PrintVariantsExampleTest

Anders Leung
authored and
cmnbroad
committed
Add javadoc

Anders Leung
authored and
cmnbroad
committed
Address some review comments

Anders Leung
authored and
cmnbroad
committed
Add an encoder and write support for the VCF4.3 HtsCodec.
cmnbroad
committed
Remove obsolete VCFHeaderVersion method.
cmnbroad
committed
Unify validation failure framework.
cmnbroad
committed
Fix spotbugs issue.
cmnbroad
committed
Preserve more context for header mergers that fail due to version validation.
cmnbroad
committed