Use htslib - #5

Merged

robert-vogel merged 60 commits into

mainfrom

Mar 26, 2026

Commits on Nov 18, 2025

intermediate update
robert-vogel
committed
af83fdc

Commits on Nov 19, 2025

intermediate progress on using htslib for reading vcf, vcf.gz, bcf files.
robert-vogel
committed
907d0ee
update for reading bcf header
robert-vogel
committed
24a0f80
added retrieval of sample names
robert-vogel
committed
c3c6730

Commits on Dec 11, 2025

updates
robert-vogel
committed
053d877

Commits on Dec 12, 2025

added options for different matrices, made place holders for computations that I need to complete.
robert-vogel
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d82567f
IMPORTANT: not working. Added logger tool and applied to the main.cpp. I can run the program and all inputs but --help are parsed correctly.
robert-vogel
committed
e238d21

Commits on Dec 13, 2025

Commits on Dec 16, 2025

added record parsing, but no computations are complete, just trying to correctly extract data.
robert-vogel
committed
7c5ab04

Commits on Dec 17, 2025

intermediate progress, still not operational
robert-vogel
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c26fb86
intermediate update
robert-vogel
committed
d7227e9
update BcfRecord to BcfFloatRecord
robert-vogel
committed
5328e99

Commits on Dec 18, 2025

intermediate upate
robert-vogel
committed
b1bb96e

Commits on Dec 19, 2025

increase code warnings and errors at compile time.
robert-vogel
committed
119d3a3

Commits on Dec 23, 2025

Intermediate and temporary update
robert-vogel
committed
919904c

Commits on Jan 2, 2026

updated subcommands for both contig matrix calculation and loco
robert-vogel
committed
81d1eb6

Commits on Jan 3, 2026

Commits on Jan 7, 2026

unfinished update
robert-vogel
committed
ab22949

Commits on Jan 13, 2026

intermediate commit to move code to another dev environment.
robert-vogel
committed
04c7855

Commits on Jan 15, 2026

intermediate update.
robert-vogel
committed
9ebb4b9

Commits on Jan 20, 2026

intermediate commit
robert-vogel
authored
adbb2ff

Commits on Jan 23, 2026

incomplete update and reorganization of grm and i/o. does not compile, intermediate update
robert-vogel
authored
0e1c9a9

Commits on Jan 26, 2026

updating writing for better use of claude code, the agentic AI coding assistant.
robert-vogel
authored
821a58a

Commits on Jan 27, 2026

Commits on Jan 29, 2026

Update:
robert-vogel
authored
3a98669

Commits on Jan 30, 2026

Commits on Feb 2, 2026

Commits on Mar 18, 2026

Commits on Mar 19, 2026

added grm read /write code, update for size_t -> uint64_t, versioning structures
robert-vogel
committed
ba44450

Commits on Mar 20, 2026

debug careless errors.
robert-vogel
committed
0f90443
debugging more careless errors.
robert-vogel
committed
2f07e7e
debug grm io so that it compiles, and started writing unit tests.
robert-vogel
committed
b4ef2c1

Commits on Mar 21, 2026

Commits on Mar 22, 2026

Commits on Mar 26, 2026