perf(long): pipe minimap2 straight into the plasmid FASTQ extraction (removes the last SAM in long mode)

[sanjaynagi-eit]

Stacked on #3 — it uses ExternalTool.run_piped from that PR, so it is based on perf/pipe-minimap-to-sort rather than main. Review #3 first.

Problem

#3 removed the intermediate SAM from the depth mappings. This is the other one.

In long-only mode:

samfile = Path(outdir) / "long_read.sam"
minimap_long_reads(input_long_reads, fasta, samfile, ...)   # writes the whole SAM
...
extract_long_fastqs_fast(samfile, plasmidfastqs, threads)   # samtools view | awk

long_read.sam has exactly one consumer — the samtools view | awk filter that pulls out plasmid-mapped and unmapped reads. minimap2's full uncompressed SAM is written to disk purely so samtools can read it straight back: 0.64 GiB written and re-read for a real ONT isolate, on top of the 0.64 GiB #3 already avoids in the depth mapping.

Change

map_and_extract_long_fastqs runs minimap2 | samtools view | awk as one pipeline through ExternalTool.run_piped, so nothing lands on disk between the stages.

two-step (SAM to disk)	19.7 s
piped	18.7 s
intermediate SAM avoided	0.64 GiB written + re-read

The plasmid FASTQ is byte-identical to the two-step form.

Scope

Hybrid mode is untouched. There long_read.sam is also read by sam_to_bam for split_bams, so it genuinely has two consumers and still has to exist. Only the long-only call site changes.

The awk program moves into a PLASMID_READ_AWK constant shared by the piped and the existing file-based paths. The command extract_long_fastqs_fast builds is unchanged — verified by string comparison against the original literal, since it is easy to shift a backslash while refactoring an embedded awk script.

Tests

New tests/test_long_extraction.py: the piped output hashes equal to the two-step output on real reads, no .sam is left on disk, the output is well-formed FASTQ with matching sequence and quality lengths, and the awk filter still selects flags 0/16 on plas contigs plus flag 4. All existing tests pass (77 non-slow).