Shane McCarthy comments

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                                            Shane McCarthy

indexcov support for csi indexes

Cool. Thanks!

Extracting blocks of unaligned reads from CRAM

@jkbonfield Can I resurrect this thread? The 100Gbp+ data coming off the PacBio Sequel II and ONT PromethION means that we are getting large unaligned files at the moment to...

Does probaln_glocal() use the wrong emission probability for N?

cc @lh3

`samtools faidx` fails to retrieve large scaffolds

Thanks @daviesrob. Pulled in the current develop head(s) and still fails to retrieve `scaffold_8` and larger... Let me know if you want the location of the file on Sanger disk...

`samtools faidx` fails to retrieve large scaffolds

Have sent you an email.

`samtools faidx` fails to retrieve large scaffolds

Thanks to @daviesrob identified that this was because I was running out of memory on the node - running on a node with enough memory worked as expected.

`seqtk seq` segfaults on 10G scaffolds

@c-zhou has added a 64-bit version of `seqtk` here: c-zhou/seqtk64@25c656cc6a9e48ab45cd39a9c6c74c48b4cf694b @lh3, would you be open to pulling this in, or better to leave as a `seqtk64` fork?

not compiling because of DB_CSS to DB_CCS change

Thanks @thegenemyers. Note DEXTRACTOR here also needs updating with the same fix. Not just in DASCRUBBER. Sorry, I kind of dropped off with the palindrome adapters thing. Yes, would be...

[1.2.0 - Ancient Destiny] Chunk fasta reads for better parallelization for revio pacbio data

@yumisims @DLBPointon. Maybe use https://nf-co.re/modules/seqkit_split2 ?

[1.2.0 - Ancient Destiny] Chunk fasta reads for better parallelization for revio pacbio data

`seqkit split2` is multithreaded and will output gzipped chunks