quick fix for broken read (mapped to no ref bases)

[tedsharpe]

there is a read with the cigar 44I107S, which is complete gibberish, in the NA12878 bam.
it's nonsense, but we can't afford to blow up.

[SHuang-Broad]

Is there a way to drop such reads, considering it is in such an incoherent state?

[tedsharpe]

Not easy, because then we'll have a read that claims to be part of a pair but which has no mate, for example. It'll mess up other stuff.

[SHuang-Broad]

For documentation purposes, can you post the SAM record of the offending read here?

[codecov-io]

Codecov Report

Merging #3662 into master will decrease coverage by 0.002%.
The diff coverage is 0%.

@@               Coverage Diff               @@
##              master     #3662       +/-   ##
===============================================
- Coverage     79.264%   79.263%   -0.002%     
  Complexity     17394     17394               
===============================================
  Files           1144      1144               
  Lines          62930     62930               
  Branches        9551      9551               
===============================================
- Hits           49881     49880        -1     
  Misses          9241      9241               
- Partials        3808      3809        +1

Impacted Files	Coverage Δ	Complexity Δ
.../hellbender/tools/spark/sv/utils/SVFastqUtils.java	64.646% <0%> (-0.505%)	5 <0> (ø)

[tedsharpe]

HJYFJCCXX160204:4:2122:2646:19786	163	2	233750853	70	44I107S	=	233750920	214	GTGTATGCATGTGCGGTGTGTACGGTGTGATGTATGTGCCATGTTTGTGCATGTGTGCTGTGTATACACGTGTGCAGTGTTGTGTGCCGTGCATATGTGCAGAGTGGTGTGTGTGGGTGTGGTGTGTGTGGGCAGGCGGGGGGTGTGCTGG	=?>???>>=?>>==8=>====>=8=3;==<>>>>>>>:>><<;>;>>>>>>/60><>=?;82><=6;:%%8><2./4;;>???;;>=/&<<############################################################	MC:Z:4S147M	OC:Z:29M4D15M107S	PG:Z:MarkDuplicates.1N	RG:Z:HJYFJ.4	NM:i:44	MQ:i:60	OQ:Z:AAFFFKKKAFKFKKFKKKKKKKKKK<AKKKFFKFKFKAKKA<AF<FKKKKK,<,FAFFKA77FAA7F<,,7FA77,7<AFKKKA<FF7,AA############################################################	UQ:i:0	AS:i:29

EDITED_FOR_EYEBALLING

[cwhelan]

:+