Fix simple cases of invalid cigars

andreas-wilm / lofreq3

LoFreq Version 3

MIT License

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Open andreas-wilm opened 4 years ago

andreas-wilm commented 4 years ago

i.e. leading/trailing indel before/after matches
See e.g. 1I99M for EAS20_8_6_87_382_926 in spike-in.bam
first classify problems in real data (spike-in.bam was massaged with bamsurgeon)

andreas-wilm commented 4 years ago

Possibly just BAMsurgeon artefacts