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VCF Overhaul #105

Merged
merged 27 commits into from
Sep 27, 2021
Merged

VCF Overhaul #105

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cb0282d
moving functions from VCFWriter to VCFHeader as appropriate as well a…
charlesgregory Sep 1, 2021
5c5f984
added HeaderRecord and unittests
charlesgregory Sep 1, 2021
f05b737
HeaderRecord now helps with creation of new header lines
charlesgregory Sep 2, 2021
00c2802
bug fix for HeaderRecord
charlesgregory Sep 2, 2021
da8f1f8
added removeFormat and more test coverage for VCFRecord
charlesgregory Sep 2, 2021
96925e6
fixed #69
charlesgregory Sep 2, 2021
5944871
more fixes and test coverage
charlesgregory Sep 2, 2021
66b0fe9
bug fix in vcf reader along with more tests
charlesgregory Sep 4, 2021
29e3f5e
added getters for Info and Format fields along with structs to repres…
charlesgregory Sep 5, 2021
809f058
added new enums, renamed other enums, and reorganize
charlesgregory Sep 5, 2021
8dc02a0
a few more functions, bug fixes, and unittests
charlesgregory Sep 5, 2021
9327bda
added comments
charlesgregory Sep 5, 2021
80f3d53
once again a new function and more unittest coverage
charlesgregory Sep 5, 2021
5defd0f
comment fixes
charlesgregory Sep 5, 2021
d23bb12
dhtslib.vcf enums values are now set by htslib enums
charlesgregory Sep 7, 2021
9e8ea83
VCF enums changed from ALL_CAPS to Capitalized and some enums names w…
charlesgregory Sep 7, 2021
05df831
corrected comments
charlesgregory Sep 7, 2021
f75b6e7
unpack method and unittests to confirm unpack level
charlesgregory Sep 7, 2021
50a3f67
potentially controversial, setting default unpack value for VCFReader…
charlesgregory Sep 7, 2021
f2b29df
added bcf_hdr_sync to a function
charlesgregory Sep 7, 2021
99f6949
UnpackLevels -> UnpackLevel
charlesgregory Sep 10, 2021
e91d936
InfoField and FormatField changes
charlesgregory Sep 10, 2021
0910089
some more protection around filter setting and getting to prevent und…
charlesgregory Sep 10, 2021
1056615
comment updates, removed old function from VCFReader, and moved vcfve…
charlesgregory Sep 10, 2021
e2095ac
added back some old functions with deprecated warnings and unitests
charlesgregory Sep 10, 2021
b8873fa
print to see why its failing on github actions
charlesgregory Sep 10, 2021
1768e09
changed unittest as VCFWriter adds a filedate and on github actions i…
charlesgregory Sep 10, 2021
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