PR to speed up long read mapping #30

[codecov[bot]]

Codecov Report

Patch coverage: 62.20% and project coverage change: +20.86% :tada:

Comparison is base (2c85db8) 55.89% compared to head (464da11) 76.75%.

:exclamation: Current head 464da11 differs from pull request most recent head e12180f. Consider uploading reports for the commit e12180f to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #33 +/- ## =========================================== + Coverage 55.89% 76.75% +20.86% =========================================== Files 17 19 +2 Lines 1535 1777 +242 Branches 178 210 +32 =========================================== + Hits 858 1364 +506 + Misses 625 326 -299 - Partials 52 87 +35 ``` | [Files Changed](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras) | Coverage Δ | | |---|---|---| | [src/plassembler/utils/external\_tools.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL2V4dGVybmFsX3Rvb2xzLnB5) | `69.62% <20.00%> (-1.62%)` | :arrow_down: | | [src/plassembler/utils/run\_canu.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL3J1bl9jYW51LnB5) | `24.19% <24.19%> (ø)` | | | [src/plassembler/utils/run\_dnaapler.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL3J1bl9kbmFhcGxlci5weQ==) | `36.36% <36.36%> (ø)` | | | [src/plassembler/\_\_init\_\_.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL19faW5pdF9fLnB5) | `81.85% <66.25%> (+44.17%)` | :arrow_up: | | [src/plassembler/utils/input\_commands.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL2lucHV0X2NvbW1hbmRzLnB5) | `69.09% <70.37%> (+29.94%)` | :arrow_up: | | [src/plassembler/utils/plass\_class.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL3BsYXNzX2NsYXNzLnB5) | `77.43% <75.00%> (+18.53%)` | :arrow_up: | | [src/plassembler/utils/cleanup.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL2NsZWFudXAucHk=) | `79.51% <78.94%> (+62.85%)` | :arrow_up: | | [src/plassembler/utils/db.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL2RiLnB5) | `83.78% <82.00%> (+3.78%)` | :arrow_up: | | [src/plassembler/utils/depth.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL2RlcHRoLnB5) | `97.70% <100.00%> (+2.29%)` | :arrow_up: | | [src/plassembler/utils/sam\_to\_fastq.py](https://app.codecov.io/gh/gbouras13/plassembler/pull/33?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras#diff-c3JjL3BsYXNzZW1ibGVyL3V0aWxzL3NhbV90b19mYXN0cS5weQ==) | `72.15% <100.00%> (+1.09%)` | :arrow_up: | ... and [3 files with indirect coverage changes](https://app.codecov.io/gh/gbouras13/plassembler/pull/33/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=George+Bouras)

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