Rope bwt to read mapping #274
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #274 +/- ##
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+ Coverage 80.78% 80.91% +0.13%
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Files 95 95
Lines 7202 7159 -43
Branches 1205 1190 -15
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- Hits 5818 5793 -25
+ Misses 918 906 -12
+ Partials 466 460 -6 ☔ View full report in Codecov by Sentry. |
smm477
approved these changes
Jan 17, 2025
tcasstevens
reviewed
Jan 17, 2025
| .filter { it.name.endsWith("h.vcf") || it.name.endsWith("h.vcf.gz") }.map { "${hvcfDir}/${it.name}" } | ||
| .toList() | ||
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| val graph = HaplotypeGraph(hvcfFiles) |
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Maybe I should add a constructor that takes a directory?
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Yeah I have had to do this a number of times and it would be very helpful just to pass a directory path.
tcasstevens
approved these changes
Jan 17, 2025
btmonier
approved these changes
Jan 23, 2025
docs/imputation_ropebwt.md
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| !!! note | ||
| This document is a work in progress and will be updated as the | ||
| imputation pipeline is further developed. Please check back for | ||
| updates. As of now the pipeline is in a BETA state but is functional. |
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Indent the paragraph in the note block so its lined up with the note id. For example:
!!! note
Notes go here...
docs/imputation_ropebwt.md
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| updates. As of now the pipeline is in a BETA state but is functional. | ||
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| In this document, we will discuss the steps needed to perform | ||
| imputation using the ropebwt3 tool within the PHG. The steps: |
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Add reference link to ropebwt3:
[ropebwt3](https://github.com/lh3/ropebwt3)
docs/imputation_ropebwt.md
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| !!! note | ||
| The steps detailed in this document build on the materials from | ||
| the "[Building and Loading](build_and_load.md)" documentation. | ||
| Please review this if you have not worked with the PHG before! |
docs/imputation_ropebwt.md
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| !!! note | ||
| This step is currently needed, but will be removed in the future as | ||
| we can do direct connections to the hVCF TileDB instance. |
docs/imputation_ropebwt.md
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| !!! note | ||
| The following steps in the rest of this document will assume we are | ||
| in the top level of our `phg_v2_example` working directory. |
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