Fix incorrect assignment of features to SV

[likhitha-surapaneni]

ENSVAR-6804

Testing

chr6    32345991    MantaDEL:62282:0:0:0:0:0    TGTCATATCCTCATTTTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCCGGACTGCGGACTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCCGCTTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGTGCCCGCCACAGCGCTCGGCTAATTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC    T   661
chr6    32446649    MantaBND:30158:1:2:0:0:0:0  G   [CHRX:31982956[G    512 SVTYPE=BND;MATEID=MantaBND:30158:1:2:0:0:0:1;BND_DEPTH=55;MATE_BND_DEPTH=50 GT:FT:GQ:PL:PR:SR   0/1:PASS:512:562,0,602:25,2:48,16

[nakib103]

@likhitha-surapaneni , it fixes the issue as expected 👍

But, I was testing it with gnomAD SV file with first 10000 variant with and without the fix.

The result differ much and there is lot less variant in the output file with this PR than without this PR. For example the following variant would get missed completely -

chr1    1687504 gnomAD-SV_v3_BND_chr1_00034905  N       <BND>

But if you change the buffer size (say 50) the above variant gets annotated. So somehow it is affected by buffer size.