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Samtools #47

Merged
merged 4 commits into from
Jan 1, 2024
Merged

Samtools #47

merged 4 commits into from
Jan 1, 2024

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Koeng101
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@Koeng101 Koeng101 commented Jan 1, 2024

Adds samtools to minimap2

Koeng101 and others added 4 commits January 1, 2024 13:50
* minimally functioning sam parser

* Update io/sam/sam.go

Co-authored-by: Willow Carretero Chavez <[email protected]>

* few udpates from comments

* Update io/sam/sam.go

Co-authored-by: Willow Carretero Chavez <[email protected]>

* Update io/sam/sam.go

Co-authored-by: Willow Carretero Chavez <[email protected]>

* add validate

* Update io/sam/sam.go

Co-authored-by: Willow Carretero Chavez <[email protected]>

* fixed sam_test

* Add in bio parser

* Updated sam to be in bio

* add package level docs

* Wrote WriteTo, still need testing

* make linter happy

* Noted Validate as not implemented

* add validate function

* fully test validate functions

* fixed mapq and added more coverage

---------

Co-authored-by: Willow Carretero Chavez <[email protected]>
@Koeng101
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Koeng101 commented Jan 1, 2024

Need to add documentation, but this seems to work.

@Koeng101 Koeng101 merged commit 01b183e into minimap2 Jan 1, 2024
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@Koeng101 Koeng101 deleted the samtools branch January 1, 2024 22:35
Koeng101 added a commit that referenced this pull request Jan 2, 2024
* init minimap2

* add test-lib

* Samtools (#47)

* add samtools (without documentation) to minimap2 branch.

* add better docs to samtools
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