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alignments contain empty positions and this causes problems #1503

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ekg opened this issue Mar 7, 2018 · 0 comments
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alignments contain empty positions and this causes problems #1503

ekg opened this issue Mar 7, 2018 · 0 comments

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ekg commented Mar 7, 2018

This can be resolved by removing the empty positions in JSON:

vg view -a aln.gam | sed 's/"position": {},//g' | sed 's/"position": {}//g' | vg view -JaG - >aln.fixed.gam

However, it should be fixed in the mapper's output.
@ekg ekg closed this as completed in 60d27fd Mar 12, 2018
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