Bbtools-flver To Sdm- - 

bbtools-flver-to-sdm -i flver_report.txt -o output.sdm.json --format json

from bbtools_sdm import convert
convert(flver_path="report.txt", output_path="data.sdm.parquet")

FLVer Input (snippet):

Read_1234	length=1450	expected=1500	dev=-3.3%	status=WARN
Read_5678	length=3000	expected=3000	dev=0.0%	status=PASS

SDM Output (JSON):


  "sdm_version": "1.0",
  "records": [
"entity":  "id": "Read_1234" ,
      "feature":  "length": 1450 ,
      "reference":  "length": 1500 ,
      "quality":  "deviation_percent": -3.3 ,
      "validation":  "status": "WARN" 
    ,
"entity":  "id": "Read_5678" ,
      "feature":  "length": 3000 ,
      "reference":  "length": 3000 ,
      "quality":  "deviation_percent": 0.0 ,
      "validation":  "status": "PASS"
]

The transformed data is inserted into the Sdm- target. This phase requires validation checks to ensure that referential integrity is maintained (e.g., no orphaned records).

bbtools-flver2sdm --input sample.flv --min-coverage 5 --min-quality 20 --output sample.sdm --format tsv

The phrase "To Sdm" suggests a conversion or transformation process from one format or type to another, specifically to "Sdm". SDM could stand for several things, but in bioinformatics, it might refer to a Specific DNA or protein format, or perhaps a tool/file format named SDM. Bbtools-flver To Sdm-

  • Source: sequence / basecalls -> Target: sequence

  • Source: quality_scores -> Target: quality (array of ints)

  • Source: flags / sam-like fields -> Target: attributes (map) bbtools-flver-to-sdm -i flver_report

  • Source: read_group / sample -> Target: provenance.sample

  • Source: per-base annotations (e.g., methylation) -> Target: annotations.per_base

  • Source: summary stats (coverage, length) -> Target: metrics from bbtools_sdm import convert convert(flver_path="report

    • Assumption: this phrase is ambiguous and likely encodes a transformation or mapping between two tools/formats: "Bbtools-flver" (interpreted as a variant of BBTools or a FLVER format) and "Sdm-" (interpreted as SDM, SDM format, or a Short Data Model). I assume the task is to describe a systematic conversion/interpretation process from "Bbtools-flver" to "Sdm-". Below I present a structured, actionable specification for such a conversion, with examples.

    The term "flver" could refer to a specific tool or function within the Bbtools suite. However, without more context, it's difficult to determine the exact purpose of "flver". It might be involved in tasks like genome assembly, variant calling, or gene prediction.