#350 fix overlapping imprecise breakpoints in mavis v2

[calchoo]

Fix for limiting the breakpoints start/ends when they overlap too much

[zhemingfan]

Hi @calchoo, can you lint the files and add some quick test cases for this scenario in developv2? I should have some examples at: https://github.com/bcgsc/mavis/blob/master/tests/test_mavis/convert/test_tools_vcf.py#L68

[codecov[bot]]

Codecov Report

Patch coverage: 82.45% and project coverage change: +8.72 :tada:

Comparison is base (cfc68d4) 81.52% compared to head (d8092b2) 90.24%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop_v2 #352 +/- ## ============================================== + Coverage 81.52% 90.24% +8.72% ============================================== Files 58 59 +1 Lines 10348 10599 +251 ============================================== + Hits 8436 9565 +1129 + Misses 1912 1034 -878 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `90.24% <82.45%> (+8.72%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc) | Coverage Δ | | |---|---|---| | [mavis/annotate/file\_io.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvYW5ub3RhdGUvZmlsZV9pby5weQ==) | `88.73% <ø> (+2.25%)` | :arrow_up: | | [mavis/annotate/variant.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvYW5ub3RhdGUvdmFyaWFudC5weQ==) | `92.80% <ø> (+11.91%)` | :arrow_up: | | [mavis/assemble.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvYXNzZW1ibGUucHk=) | `95.60% <ø> (+2.93%)` | :arrow_up: | | [mavis/config.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvY29uZmlnLnB5) | `88.69% <ø> (+0.50%)` | :arrow_up: | | [mavis/illustrate/util.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvaWxsdXN0cmF0ZS91dGlsLnB5) | `92.06% <ø> (ø)` | | | [mavis/pairing/pairing.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvcGFpcmluZy9wYWlyaW5nLnB5) | `95.17% <0.00%> (+11.03%)` | :arrow_up: | | [mavis/summary/summary.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvc3VtbWFyeS9zdW1tYXJ5LnB5) | `65.71% <ø> (+41.42%)` | :arrow_up: | | [mavis/tools/\_\_init\_\_.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvdG9vbHMvX19pbml0X18ucHk=) | `90.90% <ø> (ø)` | | | [mavis/validate/base.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvdmFsaWRhdGUvYmFzZS5weQ==) | `87.05% <ø> (+32.37%)` | :arrow_up: | | [mavis/tools/vcf.py](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc#diff-bWF2aXMvdG9vbHMvdmNmLnB5) | `89.56% <83.63%> (-8.03%)` | :arrow_down: | | ... and [1 more](https://app.codecov.io/gh/bcgsc/mavis/pull/352?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc) | | ... and [22 files with indirect coverage changes](https://app.codecov.io/gh/bcgsc/mavis/pull/352/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=bcgsc)

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.