Hybrid pangenome - #33
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Combine the human pangenome with sample short-read fastq and aligned long-read data for variant calling: k-mer counting across both read sets, personalized diploid graph construction with vg, graph updates with PGHapUpdateAlgo using the long-read alignments and LongReadSV calls, re-alignment of extracted short reads to the personalized pangenome with liftover, short-read dedup and metrics, and PangenomeSV + DNAscope calling with LR readgroup attributes. The dedup and metrics job builders move from SentieonPangenome to BasePangenome so both pangenome pipelines share them; the emitted dnascope-pangenome commands are unchanged. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ngenome Aligned short-read BAM/CRAM input via `--sr_aln`, mutually exclusive with fastq input. Aligned input is assumed deduplicated: no dedup or metrics jobs run, read extraction and k-mer counting share a single pass over the input (driver ReadWriter | pgutil extract | kmc, with the long-read FASTA streams concatenated), and the lifted alignment is written directly to the output. The calling stages rewrite the input readgroups with `--replace_rg` to set LR:0. Unaligned long-read (uBAM/uCRAM) input via `--lr_align_input` and `--lr_input_ref`. Each input is realigned with minimap2 using the new `minimap2_lr.model` bundle member; k-mer counting reads the original input files in parallel with the realignment. Also fix `cmd_samtools_fastq_minimap2` and `cmd_samtools_fastq_bwa` to decode the input file with `input_ref` rather than the alignment target reference, matching the flag's documented purpose. This changes behavior for dnascope-longread and dnascope-hybrid runs where the two references differ. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Replace `sort -k1,1 -k2,2n` with `bedtools sort -faidx` in the LongReadSV BED generation so the regions sort correctly for references with an unusual contig order. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Add `--pangenome_contig_prefix` (default GRCh38#0#) and pass it to PGHapUpdateAlgo, pgutil lift, and PangenomeSV so a non-default pangenome reference name uses a consistent prefix throughout. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Reject BAM/CRAM inputs with no @rg header lines (previously the LR attribute was silently never applied, or build_dag crashed), require readgroup IDs to be unique across all inputs, and report malformed @rg header lines with the offending file instead of a traceback. check_kmc_patch now parses the k-mer count from the KMC output and fails on a zero count, catching KMC builds that read nothing from piped stdin while still exiting successfully. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
In Sentieon 202503.04 the HybridStage1 `--hap_bam` output is unsorted and `-` sends it to stdout. Send the hap BAM to stdout and pipe it to `sentieon util sort`, and move the algo's fastq output to a named fifo, `stage1_hap.fq`, read by bwa in the first-stage alignment. The haplotype job runs with zero scheduler threads so it always executes concurrently with the first-stage job reading the fifo. Requires sentieon driver 202503.04 or later. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The two-DAG main() override performed its tmpdir cleanup inline after the last check_execution, so a failing run skipped it and leaked the directory. Wrap the body in try/finally, mirroring BasePipeline.main. Found by qualification (DEFECT_sentieon_pangenome_tmpdir_leak). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Restore the exit-status-only probe; the piped-KMC defect is being addressed in the KMC build itself. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Replace the hardcoded sentieon-version matrix value with
${{ vars.SENTIEON_VERSION }} in all three smoke jobs, matching the
pattern already used by the Docker workflow. Each "Install sentieon"
step now fails with an explicit error when the variable is unset,
instead of a confusing tar failure on a 404 from S3.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Add a hybrid short and long-read pangenome pipeline.