Comments (4)
tobiasrausch
commented on July 17, 2024
1
Tracy relies on Boost, HTSlib and SDSL. It is not using the Staden library.
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tobiasrausch
commented on July 17, 2024
I don't fully recall this but I think there was a major reorganisation of the SCF file structure as explained here. I am sorry I don't have time to write another SCF parser but the Staden package might have a converter from older SCF formats to newer ones.
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blex-max
commented on July 17, 2024
Thank you for the pointer. It seems the Staden program trev can convert from the old standard, but it's not a documented use case and it can only, as far as I can tell, do one file at a time! I have posted on their discussion forum but the last active post was 2020 so I'm not sure if I'll get a response. Does Tracy use any of the Staden libraries out of interest?
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blex-max
commented on July 17, 2024
Solved using undocumented utility scf_update in the Staden io library - https://github.com/jkbonfield/io_lib/tree/io_lib-1-14-1, close if you like, I've left it open as I feel like it might be useful info for others
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Related Issues (20)
- How are the base quality score generated? HOT 3
- Only single-chromosome FASTA files are supported HOT 1
- Can tracy assemble trim option be disabled? HOT 1
- Decompose doesn't give bcf file give json instead HOT 3
- Base quality and consensus generation HOT 7
- How can I provide a file with a list of input files to tracy? HOT 2
- Indigo HOT 4
- Cannot execute Tracy binary on mac HOT 5
- Bioconda tracy package runs very slowly where precompiled binary is fast HOT 2
- terminate called while attempting to run tracy on WSL HOT 1
- [feature request] Further options to control trimming with consensus HOT 5
- -p signal to noise ratio HOT 1
- Annotation error in the results generated sanger sequencer HOT 4
- `Couldn't anchor the Sanger trace in the selected reference genome.` error in tracy but not in Indigo HOT 3
- Issues Installing/Compiling on Mac HOT 2
- docker images differences between quay.io and dockerhub HOT 4
- Options for specifying overlap, 'fracmatch' in consensus subcommand
- Can tracy's consensus option be updated?
- Hemizygous calls HOT 2
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