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Security: Command Injection via kopen() pipe execution (RCE)

Status: Open.

#456 In lh3/bwa;

· jabir-dev opened on Jun 1, 2026

As increase (float) -n, get some additional alignments

Status: Open.

#454 In lh3/bwa;

· dgordon562 opened on Apr 6, 2026

massive threads slow down

Status: Open.

#447 In lh3/bwa;

· kaji331 opened on Oct 10, 2025

xa2multi.pl issue creating secondary alignments from hard-clipped primary

Status: Open.

#446 In lh3/bwa;

· sjaenick opened on Jul 9, 2025

small genome index error

Status: Open.

#445 In lh3/bwa;

· lixiang117423 opened on Jul 4, 2025

Fail to read header from fasta input

Data needed

Status: Open.

#409 In lh3/bwa;

· gustavogregoracci opened on Dec 6, 2023

bwa mem hangs after a few thousand reads

Data needed

Status: Open.

#407 In lh3/bwa;

· chrishklee opened on Nov 29, 2023

Reads with mapq=0 not mapped to the same location as their mates

Status: Open.

#405 In lh3/bwa;

· pinbo opened on Nov 3, 2023

Output reads not paired with a mixture of single end and paired end reads when using smart-pairing

Bug

Status: Open.

#403 In lh3/bwa;

· nh13 opened on Oct 6, 2023

Is this an wrong alignment score in bwa-mem alignment?

Status: Open.

#398 In lh3/bwa;

· huichanghuang opened on Aug 15, 2023

bwa mem failed to locate index files

Status: Open.

#386 In lh3/bwa;

· isabelluo opened on Feb 8, 2023

bwa mem -a and -t options are incompatible?

Status: Open.

#382 In lh3/bwa;

· yazhinia opened on Jan 3, 2023