Search results

End-to-end integration test (Case 3)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#89 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

End-to-end integration test (Case 2)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#88 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

Case 4 alignment (contigs only)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#87 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

Case 3 alignment (contigs + reads)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#86 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

Feature extractors

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#82 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

phraya align CLI (Case 2)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#78 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

Alignment executor (Case 2: reads + ref)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#77 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

SIMD diagonal fill (NEON)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#72 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

SIMD diagonal fill (SSE4.2)

ready-for-agentFully specified, AFK-readyFully specified, AFK-ready

Status: Open.

#71 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

BAM/CRAM parsing

Status: Open.

#61 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 28, 2026

Integration test: 2-sample E. coli

ready-for-humanNeeds human implementationNeeds human implementation

Status: Open.

#15 In CFSAN-Biostatistics/phraya;

· crashfrog opened on May 19, 2026