Release DotMatch 0.3.0 - #74
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| paired_fastq ? "paired-fastq" : "single-read", paired_fastq ? "canonical-read-id" : "not-applicable", | ||
| k, metric_name(metric), ambiguity_policy_name(assignment_policy), qdaln_alphabet_policy(), left_start, left_len, right_start, right_len, | ||
| left_targets.count, right_targets.count, stats.total_reads, stats.assigned_pairs, | ||
| left_targets.count, right_targets.count, stats.total_reads, stats.total_reads, stats.assigned_pairs, |
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When --left-reads/--right-reads is used, stats.total_reads is incremented once per synchronized R1/R2 pair, but this line writes that same value as both total_reads and total_pairs. The new summary schema distinguishes processed FASTQ records from synchronized pairs, so a paired run with 4 R1/R2 pairs reports total_reads: 4 instead of 8, undercounting provenance/QC for every paired FASTQ run; track reads separately or emit 2 * stats.total_reads for paired mode.
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| --summary "$TMPDIR/pair_paired_summary.json" \ | ||
| --assignments "$TMPDIR/pair_paired_assignments.tsv" | ||
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| grep '^L0\tR0\t1$' "$TMPDIR/pair_paired_counts.tsv" >/dev/null |
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In the new paired FASTQ block, these single-quoted grep patterns contain \t, which basic grep treats as a literal t rather than a tab. Since pair-count writes tab-delimited rows, make cli-test fails at the first check even when the output is correct; use actual tab characters, $'...', or awk -F '\t' as elsewhere in this script.
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Summary
dotmatch feature matrixoutputs for pre-extracted cell/feature observations.dotmatch pair-count.Validation
make testmake cli-testmake python-test(589 passed, 2 skipped)make python-package-testmake repository-readymake release-readyThe Galaxy wrapper is a local integration asset; it does not claim IUC acceptance.