feature: attemping translation with `diamond` and `BlastX`#88

Draft

gordonkoehn wants to merge 49 commits intomainfrom feature/tranlate_AA_diamond

+887-5,906

Commits on Jan 30, 2025

[fix]: Docs - adding missing dependency (#85 )

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enhance docstring
Gordon J. Köhn
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makeeing a start with blastX
Gordon J. Köhn
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add pseudo code to script
Gordon J. Köhn
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add pseudo code to script
Gordon J. Köhn
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adding sam to cleartext
Gordon J. Köhn
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get gene names
Gordon J. Köhn
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Commits on Feb 4, 2025

get reference
Gordon J. Köhn
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WIP
Gordon J. Köhn
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adding get gene referece
Gordon J. Köhn
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add padding
Gordon J. Köhn
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getting refernece lenghts
Gordon J. Köhn
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adding padding
Gordon J. Köhn
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WIP
Gordon J. Köhn
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aa insertaitons
Gordon J. Köhn
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adding aa inserations
Gordon J. Köhn
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adding alligment to aa
Gordon J. Köhn
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adding nuclotide read
Gordon J. Köhn
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handle indels
Gordon J. Köhn
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add aa insertions
Gordon J. Köhn
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added nuc insertions
Gordon J. Köhn
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got aligmend nucs
Gordon J. Köhn
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killed
Gordon J. Köhn
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Commits on Feb 5, 2025

adding in aligment
Gordon J. Köhn
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PHRE33
Gordon J. Köhn
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updat
Gordon J. Köhn
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Commits on Feb 6, 2025

realize that read in nn and nn for translation is not the same
Gordon J. Köhn
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Commits on Feb 7, 2025

got read
Gordon J. Köhn
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handle insertions and cleartext
Gordon J. Köhn
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memory optimize
Gordon J. Köhn
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fix path
Gordon J. Köhn
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verify fastq
Gordon J. Köhn
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added check and todos
Gordon J. Köhn
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swichting diamond to fasta becasue of issue parsing
Gordon J. Köhn
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ensure robust file for fastq - with pos
Gordon J. Köhn
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convert bam to fasta not fastq
Gordon J. Köhn
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change to db on disk
Gordon J. Köhn
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Commits on Feb 10, 2025

makefile
Gordon J. Köhn
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ignore
Gordon J. Köhn
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added PerfMonitor and fixed TODOs
Gordon J. Köhn
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typo and progress bar
Gordon J. Köhn
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moving conversion to process module
Gordon J. Köhn
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removing nextclade converter fns
Gordon J. Köhn
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moving genomic datastructures to process
Gordon J. Köhn
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moving genomic datastructures to process
Gordon J. Köhn
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moving ref gene fn
Gordon J. Köhn
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add batch insert to sqllite
Gordon J. Köhn
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removing silo_input_transformer
Gordon J. Köhn
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factoring out translate and align
Gordon J. Köhn
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