3.9

Adjusted Signal

3.9

Raw Pattern Score

100%

Time Factor

2026-11-01

Last Push

1.9K

Stars

Shell

Language

911.0K

Lines of Code

23.3K

Files

1.4K

Pattern Hits

2026-10-31

Scan Date

0.02

HC Hit Rate

Risk Review · Payload v1

Use each vector to guide manual verification of the underlying findings.

Payload schema: 1.0.0 · Engine: 2.0.0 · Scoring: heuristic-density-v1 · Scan date: 2026-10-31.

Cognitive Ownership Risk 4.8/100 · LOW

Can maintainers explain intent, assumptions, and trade-offs? 851 finding(s).

Hallucinated Dependency & Supply Chain Risk 0.2/100 · LOW

Are imports declared and package/API names verified? 33 finding(s).

Agent Over-Engineering Ratio 13.2/100 · LOW

Are wrappers, guards, and repeated structures necessary? 531 finding(s).

PR Review Velocity Impact 20.0/100 · LOW

Which changes need focused human review? 1409 finding(s).

What These Metrics Mean

Adjusted Signal: Legacy pattern score normalized per 1,000 scanned lines and multiplied by the repository-level time factor. It is not an estimate of AI authorship.
Raw Pattern Score: Sum of severity- and context-weighted pattern findings before applying the time factor.
Time Factor: A coarse multiplier based on repository last-push metadata. It does not identify when individual code was written.
Pattern Hits: Count of configured pattern findings. Review each location and surrounding code before acting.
HC Hit Rate: High- and critical-severity findings per scanned file. Severity is a configured detector weight, not proof of a vulnerability or authorship.
Lines / Files: Scan coverage denominators used by the legacy normalized score.

Pattern-Signal History

This chart tracks the legacy adjusted pattern score across scan runs. Changes can reflect source changes, scan coverage, or detector/scoring versions; they do not measure AI adoption or prove that a team refactored code. Compare runs only when their scoring versions are compatible. The dashed line tracks the raw pattern-hit count.

Severity Breakdown

Groups findings by configured severity weight. Severity is not a confidence estimate, security rating, or proof that a package is missing. Verify imports against the project's manifests and inspect each finding in its local design context.

CRITICAL 0HIGH 488MEDIUM 104LOW 817

Directory Score Breakdown

This horizontal bar chart shows where configured pattern scores accumulate across directories. Treat the bars as locations to inspect, not as evidence of authorship or code quality. Use the file-level findings to decide whether a directory needs a focused ownership, dependency, complexity, or review check.

Pattern Findings

The scanner identified 1409 distinct pattern matches across 13 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a detector match to inspect in context. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.

Reading the findings table: The Severity column indicates the configured finding weight (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — legacy comment-context matches receive a ×1.5 score weight. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier under the legacy scoring model.

Cross-File Repetition488 hits · 2440 pts

Severity	File	Line	Snippet	Context
HIGH	recipes/diatracer/diatracer.py	0	please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfr	STRING
HIGH	recipes/msfragger/msfragger.py	0	please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfr	STRING
HIGH	recipes/ionquant/ionquant.py	0	please provide pass a license key with the --key argument. you may obtain a key by agreeing to the terms at https://msfr	STRING
HIGH	recipes/diatracer/diatracer.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biotransformer/biotransformer.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/mobster/mobster-to-vcf.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/mobster/mobster.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-vcfstats/biopet-vcfstats.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-vcfstats/1.0/biopet-vcfstats.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-vcfstats/1.1/biopet-vcfstats.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-vcfstats/1.2/biopet-vcfstats.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/vcf2genome/vcf2genome.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/mpa-server/mpa-server.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/topas/topas.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-basecounter/biopet-basecounter.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-basecounter/0.1/biopet-basecounter.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/mgf-formatter/mgf-formatter.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/jmztab-m/jmztab-m.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-sampleconfig/biopet-sampleconfig.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-sampleconfig/0.2/biopet-sampleconfig.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/figtree/figtree.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	…pes/validate-fasta-database/validate-fasta-database.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	…submission-tool-validator/submission-tool-validator.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/cgview/cgview.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/goenrichment/goenrichment.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/crisper_recognition_tool/crt.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/hap-ibd/hap-ibd.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/hops/MaltExtract.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/hops/hops.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/pepgenome/pepgenome.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/examine/examine.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/sem/sem.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/clinod/clinod.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-seqstat/biopet-seqstat.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-seqstat/1.0/biopet-seqstat.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-seqstat/1.0.1/biopet-seqstat.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-seqstat/0.1/biopet-seqstat.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/haploview/haploview.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/effectivet3/effectivet3.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/np-likeness-scorer/np-likeness.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/dinosaur/dinosaur.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-validatefastq/biopet-validatefastq.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/clipandmerge/clipandmerge.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-bamstats/biopet-bamstats.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-bamstats/1.0/biopet-bamstats.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/biopet-bamstats/1.0.1/biopet-bamstats.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	…biopet-validateannotation/biopet-validateannotation.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/msgf_plus/msgf_plus.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/encyclopedia/encyclopedia.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/damageprofiler/damageprofiler.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/searchgui/searchgui.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/snpeff/snpeff.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/snpeff/5.1/snpeff.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/snpeff/5.0/snpeff.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/snpeff/5.1d/snpeff.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/snpeff/4.3.1t/snpeff.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/snpeff/4.5covid19/snpeff.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/snpeff/5.2/snpeff.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/jvarkit-msa2vcf/msa2vcf.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
HIGH	recipes/trimmomatic/trimmomatic.py	0	return the symlink-resolved, canonicalized directory-portion of path.	STRING
428 more matches not shown…

Over-Commented Block613 hits · 523 pts

Severity	File	Line	Snippet	Context
LOW	recipes/shapeit5/sse2neon.h	21	* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE	COMMENT
LOW	recipes/shapeit5/sse2neon.h	41	// Devin Hussey (easyaspi314) <husseydevin@gmail.com>	COMMENT
LOW	recipes/shapeit5/sse2neon.h	61	/* _mm_min\|max_ps\|ss\|pd\|sd */	COMMENT
LOW	recipes/shapeit5/sse2neon.h	81	#ifndef SSE2NEON_INCLUDE_WINDOWS_H	COMMENT
LOW	recipes/shapeit5/sse2neon.h	101	#define ALIGN_STRUCT(x) __declspec(align(x))	COMMENT
LOW	recipes/shapeit5/sse2neon.h	121	#warning "GCC versions earlier than 10 are not supported."	COMMENT
LOW	recipes/shapeit5/sse2neon.h	141	/* If using MSVC */	COMMENT
LOW	recipes/shapeit5/sse2neon.h	221	#else /* MSVC */	COMMENT
LOW	recipes/shapeit5/sse2neon.h	241	#elif defined(__aarch64__) \|\| defined(_M_ARM64)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	261	#include <arm_neon.h>	COMMENT
LOW	recipes/shapeit5/sse2neon.h	301	#define HAS__builtin_popcountll 1	COMMENT
LOW	recipes/shapeit5/sse2neon.h	341	#define vshuffleq_s16(a, b, ...) _sse2neon_shuffle(int16x8_t, a, b, __VA_ARGS__)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	361	#define _MM_FROUND_NEARBYINT (_MM_FROUND_CUR_DIRECTION \| _MM_FROUND_NO_EXC)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	401	// __int64 is defined in the Intrinsics Guide which maps to different datatype	COMMENT
LOW	recipes/shapeit5/sse2neon.h	421		COMMENT
LOW	recipes/shapeit5/sse2neon.h	441	#define vreinterpretq_m128i_s8(x) vreinterpretq_s64_s8(x)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	461	#define vreinterpretq_u32_m128i(x) vreinterpretq_u32_s64(x)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	481	#define vreinterpret_u64_m64(x) vreinterpret_u64_s64(x)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	501	#define vreinterpretq_u32_m128d(x) vreinterpretq_u32_f64(x)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	521	#endif	COMMENT
LOW	recipes/shapeit5/sse2neon.h	881	return vreinterpretq_u64_p128(vmull_p64(a, b));	COMMENT
LOW	recipes/shapeit5/sse2neon.h	981		COMMENT
LOW	recipes/shapeit5/sse2neon.h	1101	#endif	COMMENT
LOW	recipes/shapeit5/sse2neon.h	1401	// Compare the lower single-precision (32-bit) floating-point elements in a and	COMMENT
LOW	recipes/shapeit5/sse2neon.h	1621		COMMENT
LOW	recipes/shapeit5/sse2neon.h	1721		COMMENT
LOW	recipes/shapeit5/sse2neon.h	1861	vreinterpret_m64_s16(vset_lane_s16((b), vreinterpret_s16_m64(a), (imm)))	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2201	// Compute the bitwise OR of packed single-precision (32-bit) floating-point	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2221	// the lower element of dst.	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2241	// values in dst.	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2301	// b, then horizontally sum each consecutive 8 differences to produce four	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2321	// Additional Netwon-Raphson iteration for accuracy	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2561	_sse2neon_return(vreinterpret_m64_s16(ret));)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2741	// Store the lower single-precision (32-bit) floating-point element from a into	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2861	#define _mm_ucomilt_ss _mm_comilt_ss	COMMENT
LOW	recipes/shapeit5/sse2neon.h	2881		COMMENT
LOW	recipes/shapeit5/sse2neon.h	3101		COMMENT
LOW	recipes/shapeit5/sse2neon.h	3901	// Convert packed signed 32-bit integers in a to packed double-precision	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4021	#else	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4081	#endif	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4121	// element.	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4241	// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi16	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4261	#if defined(__aarch64__) \|\| defined(_M_ARM64)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4561	// of dst.	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4581		COMMENT
LOW	recipes/shapeit5/sse2neon.h	4601	// Merge the even lanes together with a 16-bit unsigned shift right + add.	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4621	// \\| \\|	COMMENT
LOW	recipes/shapeit5/sse2neon.h	4921	// Set packed double-precision (64-bit) floating-point elements in dst with the	COMMENT
LOW	recipes/shapeit5/sse2neon.h	5441	// elements) from a into memory. mem_addr must be aligned on a 16-byte boundary	COMMENT
LOW	recipes/shapeit5/sse2neon.h	5481		COMMENT
LOW	recipes/shapeit5/sse2neon.h	5561		COMMENT
LOW	recipes/shapeit5/sse2neon.h	5721	#define _mm_ucomile_sd _mm_comile_sd	COMMENT
LOW	recipes/shapeit5/sse2neon.h	5921	// Alternatively add and subtract packed double-precision (64-bit)	COMMENT
LOW	recipes/shapeit5/sse2neon.h	6021		COMMENT
LOW	recipes/shapeit5/sse2neon.h	6801		COMMENT
LOW	recipes/shapeit5/sse2neon.h	7081	// https://www.intel.com/content/www/us/en/docs/intrinsics-guide/index.html#text=_mm_extract_epi64	COMMENT
LOW	recipes/shapeit5/sse2neon.h	7121	return _mm_set_ps(floorf(f[3]), floorf(f[2]), floorf(f[1]), floorf(f[0]));	COMMENT
LOW	recipes/shapeit5/sse2neon.h	7141	{	COMMENT
LOW	recipes/shapeit5/sse2neon.h	7161	vsetq_lane_s64((b), vreinterpretq_s64_m128i(a), (imm)))	COMMENT
LOW	recipes/shapeit5/sse2neon.h	7561	// the rounding parameter, store the result as a double-precision floating-point	COMMENT
553 more matches not shown…

Self-Referential Comments44 hits · 136 pts

Severity	File	Line	Snippet	Context
MEDIUM	recipes/muset/build.sh	13	# Create the output directory	COMMENT
MEDIUM	recipes/genera/build.sh	9	# Define the Conda binary path	COMMENT
MEDIUM	recipes/ciri2/build.sh	4	# Create a binary directory in conda environment	COMMENT
MEDIUM	recipes/sqanti3/build.sh	4	# Define the isolated share directory for this specific version	COMMENT
MEDIUM	recipes/sqanti3/build.sh	7	# Create the necessary directories	COMMENT
MEDIUM	recipes/pretext-to-asm/build.sh	8	# Create the destination folder in site-packages	COMMENT
MEDIUM	recipes/fungar/build.sh	4	# Create the bin directory for executable scripts	COMMENT
MEDIUM	recipes/fungar/build.sh	7	# Create the directory for the database	COMMENT
MEDIUM	recipes/sipros/build.sh	37	# Create the siproswf script	COMMENT
MEDIUM	recipes/sipros/build.sh	44	# Create the link of extractPro.sh	COMMENT
MEDIUM	recipes/wepp/build.sh	84	# Create the wrapper script	COMMENT
MEDIUM	recipes/bramble/build.sh	24	# Create a symbolic link so both `bramble` and `bramble-rs` work	COMMENT
MEDIUM	recipes/digest/build.sh	54	# Create the Python package directory if it doesn't exist	COMMENT
MEDIUM	recipes/ciri-full/build.sh	9	# Create a wrapper script to run the jar file	COMMENT
MEDIUM	recipes/longreadsum/build.sh	9	# Create the src directory	COMMENT
MEDIUM	recipes/clincnv/build.sh	13	# Define the wrapper script path	COMMENT
MEDIUM	recipes/clincnv/build.sh	16	# Create the wrapper script	COMMENT
MEDIUM	recipes/cats-rb/build.sh	3	#Creating the bin directory	COMMENT
MEDIUM	recipes/atlas-fastq-provider/build.sh	6	# Create a config if not already present	COMMENT
MEDIUM	recipes/tncomp_finder/build.sh	3	# Create the destination directory	COMMENT
MEDIUM	recipes/tncomp_finder/build.sh	15	# Create a wrapper script in bin	COMMENT
MEDIUM	recipes/metawepp/build.sh	10	# Create the wrapper script	COMMENT
MEDIUM	recipes/tn3_ta_finder/build.sh	3	# Create the destination directory	COMMENT
MEDIUM	recipes/tn3_ta_finder/build.sh	15	# Create a wrapper script in bin	COMMENT
MEDIUM	recipes/translatory/build.sh	3	# Create the binary directory in the Conda environment	COMMENT
MEDIUM	recipes/redundans/build.sh	3	#Define the install folder and binary folder and create them	COMMENT
MEDIUM	recipes/netmd/build.sh	3	# This file is part of the Karate Club package.	COMMENT
MEDIUM	recipes/cctyper/post-link.sh	6	## Create a folder in the conda directory to host these files ("cct_data")	COMMENT
MEDIUM	recipes/gzrt/build.sh	27	# Create a temporary directory	COMMENT
MEDIUM	recipes/gzrt/build.sh	30	# Create a symlink named cc that points to $CC	COMMENT
MEDIUM	recipes/unifire/build.sh	67	# Create a wrapper to invoke it with python	COMMENT
MEDIUM	recipes/absense/build.sh	12	# Define the Conda binary path	COMMENT
MEDIUM⚡	recipes/corona_lineage_dynamics/build.sh	5	# Define the target directory	COMMENT
MEDIUM⚡	recipes/corona_lineage_dynamics/build.sh	8	# Create the target directory	COMMENT
MEDIUM⚡	recipes/corona_lineage_dynamics/build.sh	14	# Create the proxy script in $PREFIX/bin	COMMENT
MEDIUM	recipes/jacusa2/build.sh	3	# Create the installation directory	COMMENT
MEDIUM	recipes/jacusa2/build.sh	9	# Create a wrapper script named "JACUSA2" so users can run the jar directly	COMMENT
MEDIUM	recipes/neptune-signature/post-link.sh	15	# Creating a new executable (while preserving permissions). The new executable	COMMENT
MEDIUM	recipes/acedrg/build.sh	24	# Create a symlink for libmol if the upstream build installs it under libexec	COMMENT
MEDIUM	recipes/pybigtools/build.sh	26	# Creating the sdist from the monorepo placed pyproject.toml one level above Cargo.toml.	COMMENT
MEDIUM	recipes/cats-rf/build.sh	3	#Creating the bin directory	COMMENT
MEDIUM	recipes/haplink/build.sh	33	# Create a permanent depot	COMMENT
MEDIUM	recipes/reveal-tools/build.sh	11	# Create the REVEAL entry point	COMMENT
MEDIUM	recipes/hifiadapterfilt/build.sh	18	# Create an activation script for Bioconda	COMMENT

Decorative Section Separators35 hits · 135 pts

Severity	File	Line	Snippet	Context
MEDIUM	recipes/altair-mf/meta.yaml	3	# ------------------------------------------------	COMMENT
MEDIUM	recipes/ltr_retriever/build.sh	10	# -----------------	COMMENT
MEDIUM	recipes/ltr_retriever/build.sh	21	# -----------------	COMMENT
MEDIUM	recipes/scicone/build.sh	4	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/scicone/build.sh	6	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/scicone/build.sh	22	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/scicone/build.sh	24	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/phageflow/meta.yaml	34	# ── QC ───────────────────────────────────────────────────────────────────	COMMENT
MEDIUM⚡	recipes/phageflow/meta.yaml	38	# ── Host removal ─────────────────────────────────────────────────────────	COMMENT
MEDIUM⚡	recipes/phageflow/meta.yaml	44	# ── Assembly ─────────────────────────────────────────────────────────────	COMMENT
MEDIUM⚡	recipes/phageflow/meta.yaml	48	# ── Coverage ─────────────────────────────────────────────────────────────	COMMENT
MEDIUM⚡	recipes/phageflow/meta.yaml	50	# ── Viral ID ─────────────────────────────────────────────────────────────	COMMENT
MEDIUM⚡	recipes/phageflow/meta.yaml	52	# ── Quality ──────────────────────────────────────────────────────────────	COMMENT
MEDIUM⚡	recipes/phageflow/meta.yaml	57	# ── Annotation ───────────────────────────────────────────────────────────	COMMENT
MEDIUM	recipes/themis/build.sh	11	# -----------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/themis/build.sh	26	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/themis/build.sh	41	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/themis/build.sh	48	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/themis/build.sh	49	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/themis/build.sh	51	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/themis/build.sh	52	# -----------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/csem/build.sh	4	# --------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/csem/build.sh	13	# --------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/btllib/build.sh	4	# -----------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/btllib/build.sh	6	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/btllib/build.sh	39	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/btllib/build.sh	41	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/btllib/build.sh	51	# -----------------------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/btllib/build.sh	53	# -----------------------------------------------------------------------------	COMMENT
MEDIUM	recipes/unifire/post-link.sh	18	# ------------------------------------------------------------	COMMENT
MEDIUM	recipes/unifire/post-link.sh	20	# ------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/unifire/post-link.sh	37	# ------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/unifire/post-link.sh	39	# ------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/unifire/post-link.sh	44	# ------------------------------------------------------------	COMMENT
MEDIUM⚡	recipes/unifire/post-link.sh	46	# ------------------------------------------------------------	COMMENT

Deep Nesting133 hits · 133 pts

Severity	File	Line	Context
LOW	recipes/diatracer/diatracer.py	37	CODE
LOW	recipes/biotransformer/biotransformer.py	41	CODE
LOW	recipes/mobster/mobster-to-vcf.py	39	CODE
LOW	recipes/mobster/mobster.py	39	CODE
LOW	recipes/biopet-vcfstats/biopet-vcfstats.py	43	CODE
LOW	recipes/biopet-vcfstats/1.0/biopet-vcfstats.py	43	CODE
LOW	recipes/biopet-vcfstats/1.1/biopet-vcfstats.py	43	CODE
LOW	recipes/biopet-vcfstats/1.2/biopet-vcfstats.py	43	CODE
LOW	recipes/vcf2genome/vcf2genome.py	36	CODE
LOW	recipes/mpa-server/mpa-server.py	51	CODE
LOW	recipes/mpa-server/mpa-server.py	97	CODE
LOW	recipes/mpa-server/mpa-server.py	116	CODE
LOW	recipes/mpa-server/mpa-server.py	162	CODE
LOW	recipes/topas/topas.py	36	CODE
LOW	recipes/biopet-basecounter/biopet-basecounter.py	43	CODE
LOW	recipes/biopet-basecounter/0.1/biopet-basecounter.py	43	CODE
LOW	recipes/mgf-formatter/mgf-formatter.py	36	CODE
LOW	recipes/jmztab-m/jmztab-m.py	42	CODE
LOW	recipes/biopet-sampleconfig/biopet-sampleconfig.py	43	CODE
LOW	recipes/biopet-sampleconfig/0.2/biopet-sampleconfig.py	43	CODE
LOW	recipes/figtree/figtree.py	41	CODE
LOW	…pes/validate-fasta-database/validate-fasta-database.py	39	CODE
LOW	…submission-tool-validator/submission-tool-validator.py	41	CODE
LOW	recipes/cgview/cgview.py	39	CODE
LOW	recipes/goenrichment/goenrichment.py	41	CODE
LOW	recipes/hap-ibd/hap-ibd.py	41	CODE
LOW	recipes/hops/MaltExtract.py	36	CODE
LOW	recipes/hops/hops.py	36	CODE
LOW	recipes/pepgenome/pepgenome.py	38	CODE
LOW	recipes/examine/examine.py	41	CODE
LOW	recipes/bioconda-repodata-patches/gen_patch_json.py	88	CODE
LOW	recipes/sem/sem.py	40	CODE
LOW	recipes/clinod/clinod.py	39	CODE
LOW	recipes/biopet-seqstat/biopet-seqstat.py	43	CODE
LOW	recipes/biopet-seqstat/1.0/biopet-seqstat.py	43	CODE
LOW	recipes/biopet-seqstat/1.0.1/biopet-seqstat.py	43	CODE
LOW	recipes/biopet-seqstat/0.1/biopet-seqstat.py	43	CODE
LOW	recipes/haploview/haploview.py	39	CODE
LOW	recipes/effectivet3/effectivet3.py	39	CODE
LOW	recipes/dinosaur/dinosaur.py	37	CODE
LOW	recipes/biopet-validatefastq/biopet-validatefastq.py	43	CODE
LOW	recipes/clipandmerge/clipandmerge.py	36	CODE
LOW	recipes/biopet-bamstats/biopet-bamstats.py	43	CODE
LOW	recipes/biopet-bamstats/1.0/biopet-bamstats.py	43	CODE
LOW	recipes/biopet-bamstats/1.0.1/biopet-bamstats.py	43	CODE
LOW	…biopet-validateannotation/biopet-validateannotation.py	43	CODE
LOW	recipes/msgf_plus/msgf_plus.py	36	CODE
LOW	recipes/encyclopedia/encyclopedia.py	41	CODE
LOW	recipes/damageprofiler/damageprofiler.py	36	CODE
LOW	recipes/searchgui/searchgui.py	40	CODE
LOW	recipes/snpeff/snpeff.py	45	CODE
LOW	recipes/snpeff/5.1/snpeff.py	41	CODE
LOW	recipes/snpeff/5.0/snpeff.py	41	CODE
LOW	recipes/snpeff/5.1d/snpeff.py	41	CODE
LOW	recipes/snpeff/4.3.1t/snpeff.py	41	CODE
LOW	recipes/snpeff/4.5covid19/snpeff.py	41	CODE
LOW	recipes/snpeff/5.2/snpeff.py	45	CODE
LOW	recipes/jvarkit-msa2vcf/msa2vcf.py	41	CODE
LOW	recipes/trimmomatic/trimmomatic.py	40	CODE
LOW	recipes/trimmomatic/0.39/trimmomatic.py	40	CODE
73 more matches not shown…

Redundant / Tautological Comments27 hits · 40 pts

Severity	File	Line	Snippet	Context
LOW	recipes/sfold/meta.yaml	30	- sfold -h # Check if sfold command runs successfully	CODE
LOW	recipes/qualimap/build.sh	13	# Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is.	COMMENT
LOW	recipes/qualimap/build.sh	15	# Set classpath to libraries	COMMENT
LOW	recipes/qualimap/2.1.1/build.sh	13	# Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is.	COMMENT
LOW	recipes/qualimap/2.1.1/build.sh	15	# Set classpath to libraries	COMMENT
LOW	recipes/qualimap/2.2.2c/build.sh	13	# Set QUALIMAP_HOME to libraries path. This can help qualimap know where scripts/ forlder is.	COMMENT
LOW	recipes/qualimap/2.2.2c/build.sh	15	# Set classpath to libraries	COMMENT
LOW	recipes/gtdbtk/download-db.sh	47	# Check if this is overriding an existing version	COMMENT
LOW	recipes/b2btools/.run_test.sh	47	# Check if the status code is non-zero and exit with an error code	COMMENT
LOW	recipes/b2btools/.run_test.sh	61	# Check if the file is a CSV and has more than one row	COMMENT
LOW	recipes/b2btools/.run_test.sh	90	# Check if the status code is non-zero and exit with an error code	COMMENT
LOW	recipes/b2btools/.run_test.sh	104	# Check if the file is a CSV and has more than one row	COMMENT
LOW	recipes/b2btools/.run_test.sh	133	# Check if the status code is non-zero and exit with an error code	COMMENT
LOW	recipes/b2btools/.run_test.sh	147	# Check if the file is a CSV and has more than one row	COMMENT
LOW	recipes/b2btools/.run_test.sh	182	# Check if the status code is non-zero and exit with an error code	COMMENT
LOW	recipes/b2btools/.run_test.sh	196	# Check if the file is a CSV and has more than one row	COMMENT
LOW	recipes/b2btools/.run_test.sh	229	# Check if the status code is non-zero and exit with an error code	COMMENT
LOW	recipes/b2btools/.run_test.sh	243	# Check if the file is a CSV and has more than one row	COMMENT
LOW	recipes/b2btools/.run_test.sh	274	# Check if the status code is non-zero and exit with an error code	COMMENT
LOW	recipes/b2btools/.run_test.sh	288	# Check if the file is a CSV and has more than one row	COMMENT
LOW	recipes/mango/post-link.sh	3	# Set SPARK_HOME to conda installed pyspark package if not already set	COMMENT
LOW	recipes/mango/activate.sh	3	# Set SPARK_HOME to conda installed pyspark package if not already set	COMMENT
LOW	recipes/earlgrey/build.sh	47	# Set permissions to files	COMMENT
LOW	recipes/minimac4/build.sh	6	# Set CXXFLAGS to include the correct path to lzma.h and LDFLAGS to include the path to liblzma	COMMENT
LOW	recipes/haddock_biobb/post-link.sh	3	# Check if gcc is available. As gcc is hardcoded in haddock3 setup.py, it's unavailable on Bioconda tests.	COMMENT
LOW	recipes/openms-meta/build.sh	31	# Set INSTALL_RPATH to PREFIX such that there are no warnings during linkage fixing of conda-build	COMMENT
LOW	scripts/check-for-additional-platforms.sh	45	# Check if any additional platforms match this job	COMMENT

Unused Imports33 hits · 33 pts

Severity	File	Line	Context
LOW	recipes/biotransformer/biotransformer.py	12	CODE
LOW	recipes/crisper_recognition_tool/crt.py	12	CODE
LOW	recipes/pyopt/run_test.py	2	CODE
LOW	recipes/pyopt/run_test.py	3	CODE
LOW	recipes/pyopt/run_test.py	4	CODE
LOW	recipes/pyopt/run_test.py	5	CODE
LOW	recipes/pyopt/run_test.py	6	CODE
LOW	recipes/pyopt/run_test.py	7	CODE
LOW	recipes/pyopt/run_test.py	8	CODE
LOW	recipes/pyopt/run_test.py	9	CODE
LOW	recipes/pyopt/run_test.py	10	CODE
LOW	recipes/pyopt/run_test.py	11	CODE
LOW	recipes/pyopt/run_test.py	12	CODE
LOW	recipes/pyopt/run_test.py	13	CODE
LOW	recipes/pyopt/run_test.py	14	CODE
LOW	recipes/bioconda-repodata-patches/gen_patch_json.py	3	CODE
LOW	recipes/bioconda-repodata-patches/gen_patch_json.py	3	CODE
LOW	recipes/bioconda-repodata-patches/gen_patch_json.py	3	CODE
LOW	recipes/np-likeness-scorer/np-likeness.py	12	CODE
LOW	recipes/transabyss/setup.py	1	CODE
LOW	recipes/transabyss/setup.py	2	CODE
LOW	recipes/transabyss/setup.py	2	CODE
LOW	recipes/mango/run_test.py	2	CODE
LOW	recipes/mango/run_test.py	3	CODE
LOW	recipes/mango/run_test.py	4	CODE
LOW	recipes/mango/run_test.py	5	CODE
LOW	recipes/mango/run_test.py	6	CODE
LOW	recipes/fseq/fseq.py	14	CODE
LOW	recipes/fseq/fseq.py	18	CODE
LOW	…cipes/jvarkit-wgscoverageplotter/wgscoverageplotter.py	12	CODE
LOW	recipes/pysam/run_test.py	1	CODE
LOW	recipes/gemoma/GeMoMa.py	12	CODE
LOW	recipes/bamr/run_test.py	1	CODE

AI Slop Vocabulary14 hits · 32 pts

Severity	File	Line	Snippet	Context
LOW	recipes/cactus/build.sh	63	# cactus-gfa-tools is required but doesn't have tags. They just use exact commits in their scripts	COMMENT
MEDIUM	recipes/bioconductor-visiumstitched/meta.yaml	80	description: This package provides helper functions for working with multiple Visium capture areas that overlap each o	CODE
MEDIUM	recipes/r-genekitr/meta.yaml	95	# Description: Provides features for searching, converting, analyzing, plotting, and exporting data effortlessly by inpu	COMMENT
MEDIUM	recipes/delve-bio/meta.yaml	9	url: https://github.com/berndbohmeier/delve/archive/v{{ version }}.tar.gz	CODE
MEDIUM	recipes/delve-bio/meta.yaml	34	home: https://github.com/berndbohmeier/delve	CODE
MEDIUM	recipes/bwa-mem3/build.sh	83	# bundled MI_OVERRIDE=ON libmimalloc.a is the only robust override on Linux,	COMMENT
MEDIUM	recipes/bioconductor-flames/meta.yaml	166	# see run_test.r for more comprehensive test	COMMENT
MEDIUM	recipes/tapestry/meta.yaml	8	url: https://github.com/johnomics/tapestry/archive/v{{ version}}.tar.gz	CODE
MEDIUM	recipes/tapestry/meta.yaml	38	home: https://github.com/johnomics/tapestry	CODE
MEDIUM	recipes/tapestry/meta.yaml	43	dev_url: https://github.com/johnomics/tapestry	CODE
MEDIUM	recipes/enzywizard-energy/meta.yaml	41	# OpenMM can leverage CUDA if available in the environment.	COMMENT
MEDIUM	recipes/robust-pcst/meta.yaml	9	url: https://github.com/bionetslab/robust/archive/refs/tags/v{{ version }}.tar.gz	CODE
MEDIUM	recipes/robust-pcst/meta.yaml	44	home: https://github.com/bionetslab/robust	CODE
MEDIUM	recipes/robust-pcst/meta.yaml	45	dev_url: https://github.com/bionetslab/robust	CODE

Slop Phrases9 hits · 17 pts

Severity	File	Line	Snippet	Context
MEDIUM	recipes/bioconductor-breakpointrdata/meta.yaml	36	summary: Strand-seq data for demonstration purposes	CODE
LOW	recipes/mccortex/run_test.sh	9	# let's make sure to check both k-mer sizes were compiled	COMMENT
MEDIUM	recipes/bioconductor-aneufinderdata/meta.yaml	35	summary: WGSCS Data for Demonstration Purposes	CODE
MEDIUM	recipes/bioconductor-aneufinderdata/meta.yaml	36	description: Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.	CODE
MEDIUM	recipes/bioconductor-targetsearchdata/meta.yaml	36	description: Example files of GC-MS data for the TargetSearch Package. The package contains raw NetCDF files from a E.	CODE
MEDIUM	recipes/bioconductor-chromstardata/meta.yaml	35	summary: ChIP-seq data for Demonstration Purposes	CODE
MEDIUM	recipes/bioconductor-chromstardata/meta.yaml	36	description: ChIP-seq data for demonstration purposes in the chromstaR package.	CODE
MEDIUM	recipes/bioconductor-prebsdata/meta.yaml	36	description: 'This package contains data required to run examples in ''prebs'' package. The data files include: 1) Sma	CODE
LOW	recipes/optitype/config.ini	11	# environment OptiType is run, so make sure to include it in PATH.	COMMENT

Modern AI Meta-Vocabulary4 hits · 12 pts

Severity	File	Line	Snippet	Context
MEDIUM	recipes/pan_te/build.sh	20	# strip caches / logs / local tooling config / dev-only scaffolding that should never ship	COMMENT
MEDIUM	recipes/masurca/build.sh	44	# scaffolding, FLYE_ASSEMBLY=1). The bundled copy is Flye 2.5, whose launcher	COMMENT
MEDIUM	recipes/bioflowkit/meta.yaml	8	# dependencies are bioflow's small pure-Python orchestration stack.	COMMENT
MEDIUM	recipes/enzywizard-batch/meta.yaml	52	# Note: This is a meta-workflow tool that orchestrates many EnzyWizard components.	COMMENT

Hyper-Verbose Identifiers6 hits · 6 pts

Severity	File	Line	Snippet	Context
LOW	recipes/mpa-server/mpa-server.py	198	def prompt_user_for_data_download():	CODE
LOW	recipes/needletail/run_test.py	22	def test_can_parse_fasta_file(self):	CODE
LOW	recipes/needletail/run_test.py	41	def test_can_parse_fastq_file(self):	CODE
LOW	recipes/pycoverm/run_test.py	17	def test_get_coverages_from_bam(self):	CODE
LOW	recipes/bioconda-repodata-patches/gen_patch_json.py	53	def _gen_patch_instructions_per_key(index_per_key, new_index, subdir):	CODE
LOW	recipes/bioconda-repodata-patches/show_diff.py	21	def show_record_diffs_per_key(packages_key, subdir, ref_repodata, new_repodata):	CODE

Excessive Try-Catch Wrapping2 hits · 3 pts

Severity	File	Line	Snippet	Context
MEDIUM	recipes/ena-webin-cli/ena_webin_cli.py	122	print(f"Error: failed to exec java: {e}", file=sys.stderr)	CODE
LOW	recipes/ega-cryptor/ega-cryptor.py	106	except Exception as e:	CODE

Example Usage Blocks1 hit · 2 pts

Severity	File	Line	Snippet	Context
LOW	recipes/verifybamid2/verifybamid2.sh	5	# Usage:	COMMENT

bioconda/bioconda-recipes

Open-Source Code Quality, Security and Technical Debt Review