Adopt cutesv error handling #320
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@@ Coverage Diff @@
## develop_v3 #320 +/- ##
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- Coverage 86.45% 86.43% -0.02%
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Files 55 55
Lines 9289 9306 +17
Branches 2398 2404 +6
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+ Hits 8031 8044 +13
- Misses 778 779 +1
- Partials 480 483 +3
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creisle
requested changes
Mar 7, 2022
creisle
requested changes
Mar 21, 2022
creisle
reviewed
Apr 22, 2022
creisle
requested changes
Apr 26, 2022
| std_row['break2_position_start'] > std_row['break2_position_end'] | ||
| or std_row['break1_position_start'] > std_row['break1_position_end'] | ||
| ): | ||
| if 'event_type' in std_row and std_row['event_type'] != 'BND': |
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style: FYI you could just do std_row.get('event_type') != 'BND' here if you wanted
creisle
approved these changes
Apr 26, 2022
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Addresses edge cases found in SV caller outputs:
change the convert module to not allow the end of breakpoint1 to be greater than the end of breakpoint2 (
end1_after_end2)----------================---------------
----------------========---------------------
should be converted into
----------===========---------------------
----------------========---------------------
do not allow the start of breakpoint 2 to be lesser than the start of breakpoint 1 (
start2_before_start1)-------------------============---------------
----------------=================---------------------
should be converted into
-------------------============---------------
-------------------===============---------------------
breakpoint ends must allows be greater or equal to the same breakpoint start (throw a user warning in this case, as it should never happen, but still coerce the breakpoint to be the other)