Allow GBZ files to contain reference paths without haplotype numbers #4111

adamnovak · 2023-10-03T21:04:27Z

Changelog Entry

To be copied to the draft changelog by merger:

GBZ files can now hold reference paths like GRCh38#chr1, with no haplotype phase number.
vg is now compatible with jq 1.7.
Mac build should no longer fail with complaints about a missing atomic library.
Tests should no longer fail due to odd alignments from diff.

This fixes #4107.

This does nothing about #4110, which deals with the gbwt library GFA parser's lack of parsing for these path names.

adamnovak added 11 commits October 2, 2023 17:19

Use a GBWTGraph that can hold NO_HAPLOTYPE

de2fc73

Use vcflib that works on Mac C++17

abb9454

Stop using libatomic just because we can

2a3709f

Add back libatomic for GCC build

36721d0

Stop diff from aligning differently on different platforms

f8de564

Handle jq saying 1.0 instead of 1

2074895

Handle jq 1.7 removing --argfile

3162abd

Add a test for #4107

6ade88c

Keep haplotype phase number when converting to reference path

9016d97

Handle the other conversion case

268af3a

Update wiki tests to reflect new behavior

23a8736

adamnovak merged commit 49cc69c into master Oct 5, 2023
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