compgenlab / cgkit

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      "pushed_at": "2026-07-17T22:07:58Z",
      "created_at": "2026-06-18T04:47:50Z",
      "owner_type": "Organization",
      "updated_at": "2026-07-17T22:08:02Z",
      "description": "CLI for computational genomics: FASTA/FASTQ, SAM/BAM/CRAM, Oxford Nanopore workflows",
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      "name": "Computational Genomics @IndianaU",
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        {
          "tag": "v0.4.6",
          "kind": "patch",
          "published_at": "2026-07-17T16:15:58Z"
        },
        {
          "tag": "v0.4.4",
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          "published_at": "2026-07-11T04:34:19Z"
        },
        {
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        },
        {
          "tag": "v0.4.2",
          "kind": "patch",
          "published_at": "2026-06-29T23:39:00Z"
        },
        {
          "tag": "v0.4.1",
          "kind": "patch",
          "published_at": "2026-06-29T17:00:04Z"
        },
        {
          "tag": "v0.4.0",
          "kind": "minor",
          "published_at": "2026-06-27T15:00:21Z"
        },
        {
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        {
          "oid": "6f5df623efa63f5cd225bc04636df2c65dc68fbf",
          "body": "README: list all commands (add BED, Tabix, VCF groups)",
          "is_bot": false,
          "headline": "Merge pull request #6 from compgenlab/docs/readme-commands",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-17T22:07:57Z",
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        },
        {
          "oid": "b8af5c556d9c5a099311da057f0ad187d639c784",
          "body": "The command tables listed ~17 commands and predated the bed-*, tab-*/tabix-*,\nand vcf-* work: the entire BED (7), Tabix (2), and VCF (23) groups were\nmissing, along with sam-stats. Regenerate all tables from the binary's help so\ndescriptions match exactly -- now 48 commands across seven groups. Drop the\nhidden ont-umi-lookup from the advertised list, and broaden the intro to note\nVCF/variant handling.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "README: list all commands (add BED, Tabix, VCF groups)",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-17T19:08:04Z",
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        },
        {
          "oid": "72b58192cc9f97018b47efca6f42cee82471cd0d",
          "body": "all: point library dependency at github.com/compgenlab/cghts",
          "is_bot": false,
          "headline": "Merge pull request #5 from compgenlab/feature/cghts-rename",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-17T16:13:05Z",
          "body_truncated": false,
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        },
        {
          "oid": "b33a94f6cd1a4fd1b249066bbfd9049d59eafa56",
          "body": "The hts library was renamed to cghts (github.com/compgenlab/cghts, tagged\nv0.6.0). Swap the 99 imports across 53 files to the new path and re-pin\ngo.mod/go.sum to cghts@v0.6.0 via `make bump-cghts`.\n\nRename the release helper bump-hts -> bump-cghts and update the CI workflow's\n`go get ...@latest` to\n[…]\nis an internal-dependency path swap only; cgkit exposes no importable API,\nso it is invisible to users. Release as v0.4.6 (patch).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "all: point library dependency at github.com/compgenlab/cghts",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-17T15:22:57Z",
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          "oid": "a93ee0ae29f12a9cf8464dca12642660ed575b14",
          "body": "ont-polya: call per-read poly(A) sites from a strand-specific aligned BAM",
          "is_bot": false,
          "headline": "Merge pull request #4 from compgenlab/feature/ont-polya",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-16T22:44:37Z",
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        {
          "oid": "a5938d504eb50bd388e460c6570af638164986ca",
          "body": "ont-polya needs htsio.ParseCigar / CigarSoftClips / CigarQueryToRef /\nCigarAlignEnd, added in hts v0.5.5. The pin had drifted well behind (v0.4.3)\nbecause go.work masks it locally.\n\nVerified with GOWORK=off build + test, which is the only way to exercise the\npin rather than the workspace.\n\nThe v0.4.\n[…]\nf-split. BGZF is a valid gzip stream and is tabix-indexable, so this is\na strict improvement, but it belongs in the release notes.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "go.mod: bump hts to v0.5.5",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-16T22:39:25Z",
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          "oid": "aaa67b075cdc4ef51f1ae0c34ecb1915fb5fa304",
          "body": "… BAM\n\nFor each read, locate the mRNA 3' end, trace back through the poly(A) tail\nto its first A base, and report that base's 1-based genomic position -- the\npoly(A) / cleavage site. Output is one row per read: read_name, chrom,\npolya_pos, strand, plus optional polya_len / polya_source / --tag colum\n[…]\nE.md documented `ont-primers`,\nwhich has never existed (the primer command is `ont-tags`), and README was\nmissing `ont-umi-dedup`.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "ont-polya: call per-read poly(A) sites from a strand-specific aligned…",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-16T21:59:41Z",
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          "oid": "a080f996a4517360cbe72679d1a56680df29150d",
          "body": "sam-filter: unify output format under -O/--format with auto-detect",
          "is_bot": false,
          "headline": "Merge pull request #3 from compgenlab/feature/sam-filter-format-flag",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-11T04:30:56Z",
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          "oid": "a809615df8d42052a98f1b0e3955677b2e64c840",
          "body": "…-detect\n\nReplace the separate --bam / --cram boolean flags with a single\n-O/--format flag (auto|sam|bam|cram, default auto) and make the output\nargument optional.\n\nIn auto mode the format is inferred from the output extension (.bam -> BAM,\n.cram -> CRAM, otherwise SAM text); with no output file, SA\n[…]\ntput filename for SAM too.\n\nNote: this is a breaking CLI change -- the --bam and --cram flags are\nremoved in favor of -O/--format.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "sam-filter: unify output format under -O/--format with extension auto…",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-10T21:13:08Z",
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          "oid": "801fd867208341e7a136b56fac1aa7a027d2f49e",
          "body": "Add vcf-gtcount and tab-sort gzip/--skip support",
          "is_bot": false,
          "headline": "Merge pull request #1 from compgenlab/feature/vcf-gtcount",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-10T20:37:47Z",
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          "oid": "c34a1be77152bdf29244935548963576dfbcae35",
          "body": "…n-dist\n\nont-umi-cluster: floor adaptive threshold with --adaptive-min-dist",
          "is_bot": false,
          "headline": "Merge pull request #2 from compgenlab/feature/umi-cluster-adaptive-mi…",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-09T20:56:21Z",
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        {
          "oid": "533b3e1ed09413d357f4ffc0707ecbc6ff0e87b5",
          "body": "The --adaptive-threshold FPR filter excluded a distance and all higher\ndistances once the cumulative false-positive rate exceeded --adaptive-alpha.\nBecause the exclusion loop started at d=1, a small or highly-diverse UMI set\ncould exceed alpha at distance 1, drop every edge, and collapse the effecti\n[…]\nexclusion decision is gated on\nd > adaptive-min-dist. Setting --adaptive-min-dist 0 restores the previous\ncan-reach-zero behavior.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "ont-umi-cluster: floor adaptive threshold with --adaptive-min-dist",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-07-09T20:51:28Z",
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        },
        {
          "oid": "52d593532afd2b224923983a191575e3b00152af",
          "body": "Cover the two behaviors added to tab-sort: transparent gzip/BGZF input\n(round-tripped cleanly) and leading --skip header lines emitted verbatim\nahead of the data. Inputs are pre-ordered so the tests isolate the new\npaths rather than the tabix writer's ordering.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "tab-sort: test gzip input decompression and --skip pass-through",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-30T20:44:46Z",
          "body_truncated": false,
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        },
        {
          "oid": "7bf8dd268e8267ba0f354f56cb2a825efa935df8",
          "body": "Detect gzip/BGZF input by magic bytes (not filename) and decompress\ntransparently, so stdin and misnamed files work. Pass the leading --skip\nheader lines through verbatim ahead of the sorted data instead of parsing\nthem as records.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "tab-sort: transparent gzip/BGZF input and --skip header pass-through",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-30T20:41:27Z",
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        },
        {
          "oid": "8707b2e396eaa0071de828cb69223b937d01ba73",
          "body": "Rework output from a buffered wide matrix to a streaming long format\n(chrom/pos/ref/alt/gt/count, one row per genotype class) so rows can be\nwritten as each site finishes instead of all at the end.\n\nAdd parallel per-site query workers via -t/--threads (default 1; 0 or\nnegative is an error). Each wor\n[…]\n\n\nProgress (N/total sites) is written to stderr only when stderr is an\ninteractive terminal, so batch/redirected runs stay silent.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "vcf-gtcount: stream long format, add -t/--threads and TTY progress",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-30T20:40:06Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "8e0721507fb9339c7dc8fa0aea39a064be8ad0e5",
          "body": "Summarizes the per-sample GT distribution at requested sites of a\nmulti-sample, tabix-indexed VCF. Tab output is chrom/pos/ref/alt plus one\ncolumn per observed genotype class, each cell the count of samples with\nthat genotype.\n\nSites come from command-line loci (chrom:pos[:ref:alt]) and/or --sites\nF\n[…]\n genotype order with missing last.\n--passing restricts to records passing FILTER.\n\nPure cgkit (no hts change); version not bumped.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-gtcount: per-site genotype distribution across samples",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-30T16:39:07Z",
          "body_truncated": true,
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        },
        {
          "oid": "67aad8c45606d67fc961b166bbfbc40d794137a4",
          "body": "New --gtf [PREFIX:]FILE.gtf[.gz] flag (chain-ordered) plus a global --gtf-tag\nfilter, building an hts GtfAnnotator. Emits GTF_GENE/GTF_GENEID/GTF_STRAND/\nGTF_BIOTYPE/GTF_REGION/GTF_CODING/GTF_NONCODING (default prefix GTF_); gets\n--auto-convert / --alt-* for free. Bumps hts to v0.4.3.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01C7APS2Ujf7Xe7ZhEm3NFEa",
          "is_bot": false,
          "headline": "vcf-annotate: add --gtf gene annotation from a GTF file",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-29T23:34:35Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "081fda9275e59d21a732227628caaa0896ead1b9",
          "body": "Add a --auto-convert flag that matches contig names across UCSC (chr1),\nEnsembl (1), and NCBI RefSeq (NC_000001.11) naming for every external\nannotation source (BED/tab/VCF), for human primary contigs 1-22,X,Y,MT.\nThe input VCF's own contig names are not rewritten; conversion is applied\nonly when lo\n[…]\no behavior is unchanged without the flag.\n\nPin hts v0.4.2.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01DycFQn7QMmDqUXLbtSC1Hk",
          "is_bot": false,
          "headline": "vcf-annotate: add --auto-convert for cross-scheme contig matching",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-29T16:55:59Z",
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        },
        {
          "oid": "dbb13f039d399790910f648731eb572ce785a007",
          "body": "Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "gofmt: realign struct fields after the cgio->cgkit rename",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-27T14:57:52Z",
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        },
        {
          "oid": "ec4574ae0e91e5c3e8fe61730c849499cf819f09",
          "body": "These commands were developed in the v0.3.1/v0.3.2 cycles but were never\nreleased under those tags; v0.4.0 is the first release to carry them\n(alongside the cgio->cgkit rename), so their Since annotation reflects\nthat.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Mark vcf-*/tabix-index commands as Since v0.4.0",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-27T14:56:56Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "d530a285532d24bf407349516ec56bc0d8c17026",
          "body": "Rebrand the CLI from cgio to cgkit (restoring the project's original\numbrella name). hts stays a separate, importable library at\ngithub.com/compgenlab/hts (unchanged).\n\n- Module path github.com/compgenlab/cgio -> github.com/compgenlab/cgkit\n  (all internal imports + ldflags package path).\n- Binary, \n[…]\n builds still use the live go.work checkout.\n- Add `make bump-hts` and document the local/CI/release-ordering flow in\n  CLAUDE.md.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Rename cgio -> cgkit; build CI against latest hts",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-27T14:45:01Z",
          "body_truncated": true,
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        },
        {
          "oid": "85c8ca4f813144c300e1fe620d9d9787fb8e95a3",
          "body": "Both are pure CLI wiring over the existing hts SV plumbing\n(VcfRecord.AltPositions) and reference FASTA (seqio.OpenReference /\nGetSequenceRange, sequtils.ReverseComplement).\n\nvcf-tobedpe converts a structural-variant VCF to BEDPE: each ALT\nbreakpoint becomes paired intervals, with deletion-coordinat\n[…]\nd\n--bnf); the --include-ref partner-reference fetch faithfully replicates\nan ngsutilsj bug (uses the first chrom) for byte parity.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "vcf: add vcf-tobedpe and vcf-svtofasta (SV converters)",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-25T07:26:21Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "b29abd958f411659553cd02f40724585b6f5daa6",
          "body": "vcf-concat does a k-way sorted merge of coordinate-sorted VCFs that\nshare the same samples, combining their INFO/FORMAT/FILTER/ALT header\ndefinitions and erroring on overlapping positions. The two ngsutilsj\nconcat commands collapse into one: --chunks treats each argument as the\nfirst of a numbered c\n[…]\nrimary ID from a secondary (ngsutilsj NPEs on that path) and\nemits a clean distinct FILTER union (ngsutilsj's condition is buggy).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "vcf: add vcf-concat (with --chunks) and vcf-merge",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-25T07:12:39Z",
          "body_truncated": true,
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        },
        {
          "oid": "b605762c4bdf7499550bf4e522864f48615c17cd",
          "body": "Port the small, self-contained ngsutilsj VCF commands into cgio:\n\n  vcf-clearfilter   remove FILTER codes, record cleared ones in\n                    CG_CLEARED_FILTER\n  vcf-rename        rename samples in the header\n  vcf-chrfix        UCSC<->Ensembl chrom naming + contig filtering\n  vcf-remove-fla\n[…]\ncepts a sample number for the old name (ngsutilsj throws on it);\nvcf-remove-flags emits its flag-list description in header order.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "vcf: add 10 group-1 vcf-* commands",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-25T03:14:08Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "33d115774154bcf69230996719efbe4a7be8d30a",
          "body": "Expose the new hts value/flag filters as vcf-filter flags\n(--flag-present/--flag-missing, --value-missing, --eq/--neq,\n--contain/--not-contain, --in/--not-in, --lt/--lte/--gt/--gte), each\nparsed as KEY:VAL[:SAMPLE[:ALLELE]] (KEY[:SAMPLE] for --value-missing,\nCSV VAL for --in/--not-in), in command-li\n[…]\nlag-present, sample\nequality and the stats file; 11 parity cases confirm the stamped\nFILTER column is byte-identical to ngsutilsj.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "vcf-filter: wire value/flag filters and add --stats (batches 2 & 3)",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T23:21:06Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "5b290c287b591d209a52997cc37066c0ddfe1991",
          "body": "vcf-filter stamps FILTER codes by running variants through a filter chain in\ncommand-line order: --chrom-pass/--chrom-fail, --snv/--indel, --max-ins/\n--max-del, --qual, --het/--hom, with --passing/--failing output modes. The\ncommand-line-order chain helper (chainValue) is factored into vcf_chain.go and\nshared with vcf-annotate. Values are byte-identical to ngsutilsj (FILTER-code\norder normalized, as cgio uses CLI order).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-filter command (self-contained filters)",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T22:57:41Z",
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        {
          "oid": "7649efb1a22a8b7dff53a13f4ff902b79a40ec4f",
          "body": "cgio tabix-index <file.gz> builds a tabix .tbi index for an existing\nBGZF-compressed, coordinate-sorted file. Mirrors tab-sort's configuration\n(--preset bed/vcf/gff, or --seq/--begin/--end with --meta/--skip/--zero-based).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add tabix-index command",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T22:48:25Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "023b32966ecd9f19a14e5fd79979146cd98d22b7",
          "body": "Wire the FlankingBases annotator: --flanking ref.fa[:size]. Adds a small\nindexed FASTA + VCF testdata plus command and parity tests; byte-identical to\nngsutilsj.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-annotate --flanking",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T22:35:29Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "85f8138b0e083aa5db2445c7505e58b6204ba294",
          "body": "Replace the fixed annotator order with command-line order. A custom pflag.Value\n(chainValue) appends each annotator flag to a shared ordered slice as pflag sets\nit, so the exact order and interleaving are preserved (boolean chain flags set\nNoOptDefVal so they don't consume the next argument). The pi\n[…]\n so a later annotator can use a field an earlier one\nadded (e.g. --vcf GENE ... --in-file PANEL:GENE). Matches ngsutilsj behavior.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Apply vcf-annotate annotators in command-line order",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T21:36:38Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "4b44b6193d6c3b49e1c9a84387f78a03261aaf18",
          "body": "Wire InfoInFile: --in-file FLAGNAME:INFOKEY:FILE{:csv:tabcol=n}. Adds lookup\ntestdata plus command and parity tests; byte-identical to ngsutilsj.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-annotate --in-file",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T21:17:14Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "fa4d6b7554537082351ae049bd487b4c94872a4c",
          "body": "Wire the VCF-source annotator: --vcf NAME:FIELD:FILE{:!@$n}, --vcf-flag\nNAME:FILE{:!@$n}, and --vcf-id FILE. Adds source-VCF testdata plus command and\nparity tests; all variants are byte-identical to ngsutilsj.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-annotate --vcf/--vcf-flag/--vcf-id",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T18:51:55Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "88f82d19c93a94b03fe012b7df5c9a1b470d2661",
          "body": "--tab/--format-tab col, alt=, and ref= accept a header column name (resolved\nagainst the tabix file's skipped header line) in addition to a 1-based number.\nAdds header-bearing tab testdata and command/parity tests against ngsutilsj.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Support column-by-name in vcf-annotate --tab",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T18:42:22Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "dc24b552890757373cee35cd2b31af83a8a38524",
          "body": "Wire the hts TabixAnnotator into vcf-annotate: --bed and --bed-flag (BED name\ncolumn / presence), --format-bed (sample FORMAT), and --tab / --format-tab\n(any column, with col/n/alt=/ref=/collapse/first/max/extend options). BED and\ntab inputs must be tabix-indexed (bgzipped + .tbi/.csi). Column-by-na\n[…]\nlag output is byte-identical; tab values match (QUAL on untouched rows is\nnormalized, as cgio writes unmodified records verbatim).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-annotate --bed/--tab annotators",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T18:32:38Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "72bb20773e52122ffcbb28b15ccdeaca13d59be8",
          "body": "vcf-annotate runs a pipeline of annotators that add INFO/FORMAT/ID fields:\n--auto-id, --tag, --indel, --tstv, --dosage, --vardist (group A) and --vaf,\n--minor-strand, --fisher-sb, --copy-logratio (group B). Output is provenance-\nstamped. Annotator implementations live in hts/vcf/annotate; this is th\n[…]\n ngsutilsj;\ngroup B values match (FORMAT column order is cgio's stable order). --tag is\nrepeatable here (ngsutilsj is single-tag).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-annotate command (groups A & B)",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T18:17:25Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "bdd35888ff12cdd00c884dd97c0d05e6af06267a",
          "body": "New vcfcmd group porting ngsutilsj VCF commands (Since v0.3.2):\n- vcf-samples: list sample names\n- vcf-tobed: allele positions to BED (SV-aware)\n- vcf-export: INFO/FORMAT/ID/QUAL/FILTER to tab-delimited, glob + allele\n  selectors (--unique-event/--col deferred)\n- vcf-reorder: reorder/subset samples,\n[…]\nersion header lines.\n- sam-cat and sam-filter add @PG lines; ont-umi-dedup/cluster @PG lines now\n  include the cgio version (VN:).\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add vcf-* command group and file provenance stamping",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-24T16:58:22Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "fad54896ebb524ccd617b2f76c762b44b5ba8ae2",
          "body": "cgio v0.3.1's bed command group requires the hts/bed package, added in\nhts v0.3.2.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Bump hts dependency to v0.3.2",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-19T07:21:07Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "2793a25c48c0a6fb07ca240cb1b35f382e61ab60",
          "body": "Whitespace-only gofmt cleanup of files that were not gofmt-clean before.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "gofmt: align struct fields in pre-existing files",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-19T07:13:29Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "2a8066cb0f4fe3462d38f2f0a1b6f21333e224b3",
          "body": "bed-* commands (backed by the hts/bed package):\n  bed-clean, bed-tobed3, bed-tobed6, bed-resize, bed-stats, bed-tofasta,\n  and bed-set (two-file set algebra: --inter/--union/--sub/--exclusive,\n  strand-aware, --flanking, --sum/--count, provenance, BGZF/.tbi output).\n\nAlso annotate every command with\n[…]\nced in help as\n\"Since: vX.Y.Z\" via the root help template:\n  v0.1.0 fasta-*/fastq-*/seq-*/sam-*/tab-*; v0.2.0 ont-*; v0.3.1 bed-*.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add bed command group and per-command \"Since\" version annotations",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-19T06:52:32Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "35d53d5b34c4586285f14ca8a01431d9559838aa",
          "body": "Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Pin github.com/compgenlab/hts v0.3.0",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-18T04:46:05Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "0b9dfde8bf32220729519f9421290bcf8c40acee",
          "body": "Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Trim README and CLAUDE.md to CLI scope; reference hts library",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-18T04:30:23Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "5b7418e2dcab86ffc2db3948067feea1904e0f99",
          "body": "Extracted the CLI (main.go, internal/cmd/*) from cgkit into its own module\ngithub.com/compgenlab/cgio. Library imports now resolve to\ngithub.com/compgenlab/hts; binary renamed cgkit -> cgio (Makefile, CI,\nhelp text, @PG records). Copied the SAM test fixtures needed by samcmd\ninto internal/cmd/samcmd/testdata. The hts dependency resolves via the\nlocal go.work during development; a pinned require/go.sum will be added\nonce hts is published.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Rebase as standalone cgio CLI module",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-18T04:28:23Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "fc0404884134eacac2d630f9867281df2b698fcb",
          "body": "Add sam-stats command (port of ngsutils bam-stats)",
          "is_bot": false,
          "headline": "Merge pull request #27 from compgen-io/sam-stats",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-18T03:58:54Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "a9b181f9f0cb8b788e091eaa51af22651fe614aa",
          "body": "Add a sam-stats command that prints summary statistics for SAM/BAM/CRAM\nfiles: read counts, mapping rates, Q30, depth, SAM flag breakdown,\nper-reference counts, optional --tags value distributions and\n--calc-insert median. Ports the per-read logic from ngsutils bam-stats\n(unique = NH/IH/MAPQ; profil\n[…]\ne into\nPersistentPreRun so argument/flag errors still print usage while\nexecution errors do not, and stop double-printing the error in Execute.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add sam-stats command (port of ngsutils bam-stats)",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-18T03:47:12Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "96450120eae038724905dfeb73e805ed8f6ce821",
          "body": "Add GitHub project link to help footer",
          "is_bot": false,
          "headline": "Merge pull request #26 from compgen-io/help-github-link",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-15T08:14:39Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "196140e6bb99b40d0affbcfb055d2ba9b395e266",
          "body": "Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add GitHub project link to help footer",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-15T08:12:31Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "afaa1231e3780d4ecac1a106e64b2b621cc3b776",
          "body": "cgkit is its own module; an unrelated go.work in a parent directory\nwould otherwise cause \"module not in workspace\" build failures.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Makefile: disable ambient go.work so cgkit builds standalone",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-15T07:53:12Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "6949caff29bbb4e72b39c9af91ee865dcb0bbc33",
          "body": "Makefile: use find instead of rg to list Go sources",
          "is_bot": false,
          "headline": "Merge pull request #25 from compgen-io/makefile-portable-find",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T20:05:41Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "753477a1815575052215e6e7ecdfac2fa7409377",
          "body": "rg (ripgrep) is not always installed; find is portable and avoids a\nhard dependency on an external tool for the build.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Makefile: use find instead of rg to list Go sources",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T20:03:35Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "bb6c47e06678fa8a3a44080224f0acf10c7b8258",
          "body": "Replace sam-toseq with sam-tofasta/sam-tofastq; add --write-tag",
          "is_bot": false,
          "headline": "Merge pull request #24 from compgen-io/sam-tofastx-write-tag",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T19:44:56Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "24439d3f60269353223002994a7c5df999ee7373",
          "body": "Split the format-flag-driven sam-toseq into two clearly-named commands\nbacked by a shared implementation. Add --write-tag (repeatable and\ncomma-separated) to emit selected SAM tags into the read comment as\ntab-delimited tag:type:value fields; tags absent from a record are\nomitted.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Replace sam-toseq with sam-tofasta/sam-tofastq; add --write-tag",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T19:39:09Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "4243f74a666be8d594ac527394cbf43d59420bb0",
          "body": "CI: bump actions off deprecated Node.js 20",
          "is_bot": false,
          "headline": "Merge pull request #23 from compgen-io/ci-bump-actions",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T02:04:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "c77ac2b30cef6def85cb3f0f5048611408339237",
          "body": "Updates to the current major versions, all of which run on Node.js 24\n(GitHub is removing Node 20 from runners in late 2026):\n- actions/checkout v4 -> v6\n- actions/setup-go v5 -> v6\n- actions/upload-artifact v4 -> v7\n- softprops/action-gh-release v2 -> v3\n\nNo workflow input changes were required (one artifact per distinct name,\nstandard go-version-file / release inputs).\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "CI: bump actions off deprecated Node.js 20",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T02:00:34Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "a1caa800a0d6102f6da45af69de093e3e6358e4e",
          "body": "Phase 3: write-path correctness, CRAM-writer hardening, contract docs",
          "is_bot": false,
          "headline": "Merge pull request #22 from compgen-io/phase3-correctness",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T01:37:48Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "b3102dfdd2274fa6c4428da64d414a5a9a2ab032",
          "body": "Adds a static-analysis gate (Printf format checks, mutex-by-value copies,\nstruct tags, lost results, etc.) ahead of `go test`. Vet compiles the\npackages but needs no samtools; it runs after the samtools install for\nordering simplicity.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "CI: run go vet ./... before the test suite",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T01:22:00Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "21768ea6041062efdb24b24bf32ce92a0f79ba82",
          "body": "Phase 3 added htsio.ValidateCigarSeq to the CRAM writer but left the BAM\nwriter lenient. A BAM record whose CIGAR query length disagrees with len(SEQ)\nis malformed per the SAM spec, so the BAM writer now rejects it at Write time\ntoo, consistent with CRAM.\n\nReworked the UMI-dedup tests to build well-\n[…]\nth synthesizes mismatched records (UMI-dedup only rewrites the\nFlag on records read from a valid BAM), so this cannot reject legitimate output.\n\nCo-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Enforce CIGAR/SEQ validation in the BAM writer",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T01:17:43Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "e0f817985e072f6852653db647c2a070a01a64d7",
          "body": "Phase 2: malformed-input hardening across HTS I/O and codecs",
          "is_bot": false,
          "headline": "Merge pull request #21 from compgen-io/phase2-hardening",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-11T00:02:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ed8de307bb3668f0d8bdc30e3cbb45a699491176",
          "body": "Cosmetic / correctness:\n- Fix copy-pasted \"fastagcCmd\" doc comments across fasta/fastq/seq commands;\n  fix fastq-gc usage string (.fasta -> .fastq).\n- Hard rename ReverseCompliment->ReverseComplement, dnaCompliment->dnaComplement\n  and update all call sites + help text.\n- Reconcile ONT tag flags: --\n[…]\nwiseAlignmentPromise.Result against an empty batch.\n- Propagate gzip errors from gzipCompress/storeSequence instead of swallowing.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Phase 1: cosmetic cleanups + confirmed bugfixes",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-05T15:57:50Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "11674c30e3ca46959fa0adf7ee13833a6c0ad760",
          "body": "Add Windows build and source archive to releases",
          "is_bot": false,
          "headline": "Merge pull request #20 from compgen-io/rename-cgkit",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-04T18:34:13Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1ff3512cfb5f20f03a9ca3023d187f459665b531",
          "body": "Required by softprops/action-gh-release to create/update releases.\n\nAI assisted",
          "is_bot": false,
          "headline": "Restore contents: write permission for release workflow",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-04T18:32:29Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5fa28840cb3d191729d7428de7faa681fbf50598",
          "body": "samcmd had no test files, so `go test ./...` never loaded the package\nand its init() never ran. Pflag/cobra panics at init() (e.g. duplicate\nflag names) were therefore invisible to CI tests and only surfaced when\nthe binary was actually executed. A single test in internal/cmd is\nenough to load the whole subcommand tree and surface these failures\nduring `go test`.\n\nAI assisted",
          "is_bot": false,
          "headline": "Add smoke test that forces all CLI init() to run under go test",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-04T18:04:01Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "1fe832d2c745f09023da5ce77785d89e5f63ffb4",
          "body": "samReaderFlags.register() already declares --cram-ref via the shared\nfilter flag set. sam-filter was redeclaring it on the same command,\nwhich made pflag's AddFlag panic at init().\n\nsamFilterCRAMRef was never referenced after the merge — CRAM output\nisn't wired up yet — so the variable and duplicate flag were dead code.\n\nAI assisted",
          "is_bot": false,
          "headline": "Fix duplicate --cram-ref flag panic in sam-filter",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-04T18:02:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "06417d1ad11f9d1d4ef717853e9ca9662178200d",
          "body": "Add parallel BGZF compression and optimize ont-umi-dedup",
          "is_bot": false,
          "headline": "Merge pull request #18 from compgen-io/parallel-bgzf-dedup",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-04T17:49:31Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "0822d515b787907c3a043d3a26eff0029e0133ac",
          "body": "Resolved ont_umi_dedup.go conflict: both branches added a new variable\nand CLI flag (--threads here, --cram-ref on main). Kept both.\n\nAI assisted",
          "is_bot": false,
          "headline": "Merge origin/main into parallel-bgzf-dedup",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-04T17:46:38Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "4f353d8949f15840f97f4d8bdfb55507d53dfce2",
          "body": "The BAM writer iterates rec.TagOrder when present and skips any tag not\nlisted there. Newly added MI and OX tags were only being inserted into\nrec.Tags, so they never reached the output. Add SamRecord.SetTag to keep\nTags and TagOrder in sync, and use it for the new tag writes.\n\nAI assisted",
          "is_bot": false,
          "headline": "Fix dropped MI/OX tags in ont-umi-cluster output",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-06-04T17:44:28Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d9c435dd1ed48be04c77e6c005359a51fcb8f08d",
          "body": "Cram todos",
          "is_bot": false,
          "headline": "Merge pull request #17 from compgen-io/cram-todos",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-14T19:10:35Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "6863bca1ec47ed4e18158f7bec7602d1959a3998",
          "body": "AI assisted",
          "is_bot": false,
          "headline": "Document secondary/supplementary dropping and --threads in help text",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-13T14:48:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "464100c694d7a5c8f403dbd2cf7f14eebb67be23",
          "body": "- Add RefPath field to SamReaderOpts for specifying reference FASTA\n- CRAM reader now accepts and uses SamReaderOpts (was previously ignored)\n- Apply PassesFilters (flag, mapQ, tag filters) in CRAM Records() and Query()\n- Add --cram-ref flag to sam-cat, sam-filter, sam-export, sam-toseq, and\n  all O\n[…]\n mapped slice needs a ref and none is available\n  (decode time)\n- Reference provider now validates file existence at creation time\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Wire SamReaderOpts through CRAM reader, add --cram-ref flag",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-13T14:31:06Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "e2cb6abb745fa905ec33a9d79ab5c7498d3daad7",
          "body": "Secondary/supplementary alignments that appear before their primary in\ncoordinate order cannot be reliably resolved. Drop them all to avoid\nsilent data loss and eliminate the unbounded selectedNames memory growth.\nTrack count of dropped sec/supp in stats output.\n\nAI assisted",
          "is_bot": false,
          "headline": "Drop all secondary/supplementary alignments in ont-umi-dedup",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-13T12:27:53Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d6ca286e455af3265bd3c6b0701db20c8d32839f",
          "body": "Keep secondary/supplementary alignments for the selected read in each MI\ngroup and drop them for non-selected reads. Removes --keep-secondary flag\nsince this is now the default (and only) behavior.\n\nAI assisted",
          "is_bot": false,
          "headline": "Revert to always keeping secondary/supplementary for selected reads",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-13T11:10:33Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "ae2ace805f78100d1d3c831c3f4b91ace6a9e27c",
          "body": "AI assisted",
          "is_bot": false,
          "headline": "Add -t shorthand for --threads in ont-umi-dedup",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-13T01:55:45Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "21656d6985ca7e0077655bab9602fcedffe09949",
          "body": "- Add parallel BGZF writer (NewParallelWriter) with worker pool for\n  concurrent block compression and ordered drain goroutine for output\n- Make SAM, BAM, and CRAM writers thread-safe with sync.Mutex\n- Wire --threads flag through sorted BAM writer to BGZF layer\n- ont-umi-dedup: drop secondary/supplementary by default (--keep-secondary\n  to preserve), removing unbounded selectedNames memory growth\n- ont-umi-dedup: add --threads flag for parallel output compression\n\nAI assisted",
          "is_bot": false,
          "headline": "Add parallel BGZF compression and optimize ont-umi-dedup",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-13T01:15:32Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "7d2541763ad6f9dd722cf3d654d89e1ff7827ed0",
          "body": "Add contents: write permission to allow softprops/action-gh-release\nto create releases with the GITHUB_TOKEN.\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Fix GitHub Actions release permission",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-08T00:11:53Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "72541faabba5666b0c8f5f935acb8124bccbe455",
          "body": "- Add windows_amd64 build target to CI and Makefile\n- Add source zip archive to releases\n- Release assets: raw binaries + source zip\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add Windows build and source archive to releases",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T22:46:18Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "ac7a664b22d144b258bdd515e03b19d4bad52cb2",
          "body": "Rename project from cgltk to cgkit",
          "is_bot": false,
          "headline": "Merge pull request #16 from mbreese/rename-cgkit",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T22:12:36Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "d19c801a34458d04d641bc7de0cf5e0e8be40790",
          "body": "Module path: github.com/compgen-io/cgltk → github.com/compgen-io/cgkit\nBinary names: cgltk.* → cgkit.*\nAll import paths, docs, CI, and Makefile updated.\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Rename project from cgltk to cgkit",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T22:12:12Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "5ba1a634b73dfb325c15ccc1d06bb55396f922da",
          "body": "Add htsio package and ont-umi-merge command",
          "is_bot": false,
          "headline": "Merge pull request #3 from mbreese/htsio",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T21:42:18Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e63a62275000b078699427754c89d73bf6b09154",
          "body": "Add native CRAM v3 reader",
          "is_bot": false,
          "headline": "Merge pull request #13 from mbreese/working-native-cram",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T21:39:55Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "caf059a594bde4afbf6f0fcb09651735750d174f",
          "body": "Adds a proper SAM text writer in htsio/sam/ that supports writing to\nfiles or stdout (\"-\"). Also provides NewWriterFromWriter for writing\nto any io.Writer. Removes the old StdoutSamWriter from the htsio\npackage and updates sam-filter and sam-cat commands to use sam.NewWriter.\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add sam.NewWriter and remove StdoutSamWriter",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T21:28:44Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "02a54cca6453987de6b1857b9b148d15082c2e0f",
          "body": "After rebasing onto htsio, ont-umi-dedup referenced htsio.NewSamWriter\nand htsio.SamWriterOptions which don't exist on this branch (writers\nwere moved to subpackages). Updated to use bam.NewSortedWriter and\nbam.NewWriter/bam.NewReader directly.\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Update ont-umi-dedup to use bam subpackage writers",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T21:23:44Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "a2c27bdc18897223d20cbc48371749d0fc6c1afa",
          "body": "Move BAM reader/writer to htsio/bam, SAM text/samtools readers to\nhtsio/sam, tabix reader/writer and index types (Chunk, BinIndex,\nCSIIndex) to htsio/tabix. Shared types (SamRecord, SamReader,\nSamHeader, etc.) remain in htsio.\n\nNewSamReader auto-detects format via magic bytes using a reader\nregistry\n[…]\normat-specific constructors\n(bam.NewWriter, bam.NewSortedWriter, etc.).\n\nWire CRAM reader into the registry alongside BAM and SAM.\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Refactor htsio into subpackages: bam, sam, tabix",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T21:17:22Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "a4a73196091b7b0aea76de49d79ca9a1653acf01",
          "body": "- bzip2 via Go stdlib compress/bzip2\n- lzma via github.com/ulikunitz/xz (BSD-3-Clause)\n- Improve error messages for unsupported methods (rANS 4x16,\n  adaptive arithmetic, fqzcomp, name tokenizer) with human-readable\n  method names\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add bzip2 and lzma decompression support for CRAM blocks",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T21:17:22Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "547532b06ecc0ba1fa91a455271138c502566cd8",
          "body": "Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Hide ont-umi-lookup command from help output",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T19:42:16Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "987662a8a0e4b6153f8e3bc2ebd0512f247ced62",
          "body": "Writes a deduplication statistics file with summary counts (reads,\nMI groups, duplication rate), group size histogram, and per-selector-tag\ndistributions (mean/median/stdev) for kept vs discarded reads.\n\nAlso makes + optional in --best-tag (AS and AS+ both mean higher wins).\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add --stats report to ont-umi-dedup",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T17:21:11Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "8373feba1c986dd5cb95a032b50179380f56938c",
          "body": "Add ont-umi-dedup command for UMI-based PCR duplicate removal",
          "is_bot": false,
          "headline": "Merge pull request #14 from mbreese/ont-umi-dedup",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T17:10:14Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "490f3c965acc4974473c0402e7df8e043361c20c",
          "body": "Reads coordinate-sorted BAM files with MI tags (from ont-umi-cluster) and\nselects one representative read per MI group. Selection uses an ordered\nchain of criteria: --best-tag TAG (higher wins) or TAG- (lower wins),\nand --longest (aligned query length excluding soft clips). Non-selected\nreads are ei\n[…]\n removed or marked with the PCR duplicate flag (0x400).\n\nSecondary/supplementary alignments follow the fate of their primary read.\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add ont-umi-dedup command for UMI-based PCR duplicate removal",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-07T17:07:38Z",
          "body_truncated": true,
          "is_coding_agent": true
        },
        {
          "oid": "00b7f4358d10508b8898c723bcfce118607fa19a",
          "body": "Add tag order preservation and SAM/BAM round-trip tests",
          "is_bot": false,
          "headline": "Merge pull request #12 from mbreese/sam-roundtrip-tests",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-05T14:11:50Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "664448501cd482eb8f64a78c62cfd0a8883db7f5",
          "body": "- Add htsio/roundtrip_test.go with 6 test functions verifying:\n  - BAM→SAM, BAM→BAM, SAM→SAM, SAM→BAM round-trips (sha1 vs samtools)\n  - Tag order preservation through BAM write/read cycle\n  - Full field consistency through BAM write/read cycle\n- Fix sam-cat to use Records() iterator (matching updated SamReader interface)\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add round-trip tests and fix sam-cat nil opts panic",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-05T14:02:49Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "ecba06be2f1f737fd9cc14c551957a8a532e705d",
          "body": "…t data\n\n- Add TagOrder []string to SamRecord for preserving tag insertion order\n- Update parseSamLine and decodeTags to populate TagOrder\n- Update SamRecord.String() to use TagOrder when set\n- Add tagOrder parameter to encodeAuxTags, extract encodeOneTag helper\n- Add hidden sam-cat command for round-trip testing\n- Add test_tags.bam/sam with diverse tag types (Z, i, f, A, B arrays)\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Add TagOrder for consistent tag output, sam-cat command, and rich tes…",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-05T14:01:32Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "d79d7ea24ae12e021bb45ff588126a5b5662c62c",
          "body": "AI assisted",
          "is_bot": false,
          "headline": "Fix fastq-tag test for renamed FASTA/Q command group",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-04T22:45:53Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3fc943099388f0a1dd43d365bf3006825836dcb6",
          "body": "MI tags were only assigned to ~10% of reads because updateRecordUMI\nrewrote the RX tag before the MI lookup, causing the representative\nmap lookup to fail for reads with dash-separated UMIs. Move MI tag\nassignment before UMI rewriting so the lookup uses the original value.\n\nAlso merge FASTA and FASTQ command groups into a single \"FASTA/Q\" group.\n\nAI assisted",
          "is_bot": false,
          "headline": "Fix MI tag assignment bug and merge FASTA/FASTQ command groups",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-04T19:03:53Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "816073f3bf93c71e02241ecda2029d64477ad6df",
          "body": "AI assisted",
          "is_bot": false,
          "headline": "Update adaptive threshold docs for cumulative FPR and new defaults",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-04T18:29:25Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "261a6815d0ef1f34ff54d8d2705ce697151f7770",
          "body": "- New tabcmd group with tab-sort: sort tab-delimited files into\n  BGZF-compressed, tabix-indexed output with preset support (bed/vcf/gff)\n- Switch adaptive threshold to cumulative FPR (d<=1, d<=2, d<=3) so once\n  a distance fails, all higher distances are excluded too\n- Change default adaptive-alpha from 0.05 to 0.10\n- Add --no-summary-counts-index flag to disable tabix index for counts file\n\nAI assisted",
          "is_bot": false,
          "headline": "Add tab-sort command and adaptive threshold improvements",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-04T18:15:30Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "e9e8a91827e9aa9805c6233b08df236819e4f6d4",
          "body": "…23 iteration\n\nRemove the pull-style Next() method from the SamReader interface and all\nimplementations. Replace with Records() returning iter.Seq2[*SamRecord, error],\nmaking the interface fully iterator-based alongside the existing Query() method.\n\nThe sorted BAM writer merge heap now uses iter.Pull2 to convert Records()\niterators into pull functions for k-way merge access.\n\nAI assisted",
          "is_bot": false,
          "headline": "Replace SamReader.Next() with Records() iter.Seq2 for idiomatic Go 1.…",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-04T17:38:06Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "5199dddd53613a2853dee2a544a7afe1ebd08e83",
          "body": "…el jobs\n\nAI assisted",
          "is_bot": false,
          "headline": "Encode --region into MI tags to prevent overlapping IDs across parall…",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-05-04T16:59:37Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "412215d57027f1d5072e64c7911fdad23a7825ff",
          "body": "Document the native BAM/SAM/tabix reader/writer stack, BGZF package,\nindex support (BAI/TBI/CSI), Query() with iter.Seq2, and the samtools\ndependency reduction (CRAM only).\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Update README and CLAUDE.md for native HTS I/O",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-04-30T10:55:12Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "d54b1aa26386225ee4a899eedb869922448ec5e6",
          "body": "Native bam",
          "is_bot": false,
          "headline": "Merge pull request #11 from mbreese/native-bam",
          "author_name": "Marcus Breese",
          "author_login": "mbreese",
          "committed_at": "2026-04-30T10:52:07Z",
          "body_truncated": false,
          "is_coding_agent": false
        },
        {
          "oid": "3b2bc9b6038ab12917e631f39895de5d903d2dd4",
          "body": "When --summary-counts writes to a .gz/.bgz file, use TabixWriter with\nBED preset and AutoIndex instead of plain bgzf.Writer. The output is\nautomatically sorted by position and a .tbi index is generated. Plain\ntext output unchanged.\n\nCo-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>",
          "is_bot": false,
          "headline": "Use TabixWriter for sorted, indexed counts output in ont-umi-cluster",
          "author_name": "Marcus R. Breese",
          "author_login": "mbreese",
          "committed_at": "2026-04-30T10:32:07Z",
          "body_truncated": false,
          "is_coding_agent": true
        },
        {
          "oid": "4bcf5aed21961159b9ea1b7ca0834c111e08bade",
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              {
                "key": "contributor_breadth",
                "name": "Contributor breadth",
                "detail": "1 contributors",
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                "key": "openssf_scorecard_contributors",
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            "name": "Issue & PR responsiveness",
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                "status": "excluded",
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                    "code": "no_issues_or_data",
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                ],
                "max_points": 46.75
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              {
                "key": "pr_acceptance",
                "name": "PR acceptance",
                "detail": "6/6 decided PRs merged",
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                    "code": "decided_prs_merged",
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                "max_points": 38.25
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              {
                "key": "openssf_scorecard_code_review",
                "name": "OpenSSF Scorecard: Code-Review",
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          {
            "key": "stewardship",
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            "components": [
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                "key": "ownership_backing",
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              {
                "key": "verified_domain",
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              },
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                "key": "owner_reach",
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                "status": "missed",
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                ],
                "max_points": 25
              },
              {
                "key": "track_record",
                "name": "Track record",
                "detail": "12 public repos, account ~1 yr old",
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                    "code": "account_age_years",
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                ],
                "max_points": 25
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            ]
          },
          {
            "key": "package_maintenance",
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            "note": null,
            "notes": [],
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              "ecosystems": "go",
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                "key": "published_resolvable",
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                "points": 25,
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                "key": "publish_recency",
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                "key": "version_history",
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                "key": "openssf_scorecard_ci_tests",
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            "notes": [],
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                "key": "fuzzing",
                "name": "Fuzzing",
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                "key": "sast",
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                "key": "security_policy",
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                "points": 0,
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                "key": "vulnerabilities",
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                "details": [
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}