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cbg-ethz / haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
GNU General Public License v3.0
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Only provide BAM output #19

Open armintoepfer opened 7 years ago

armintoepfer commented 7 years ago

Drop all output files except for BAM. Annotate metrics to each record using custom BAM tags, such as super-read coverage or the read names of that were used.

tobiasmarschall commented 7 years ago

I agree to make BAM the default output. Having some optional "side output" such as FASTA might still be helpful.

armintoepfer commented 7 years ago

In my opinion, we can rather provide samtools one-liners to extract certain information in a different format.

tobiasmarschall commented 7 years ago

Also makes a lot of sense. That is, if we generated the according documentation.