Release 4.0.1

Fix compilation and testing on FreeBSD and MacOS.

• On BSD system, the package MUST be compiled using GCC. Otherwise the produced executable may be buggy (missing output, non-deterministic output).
• Fixed many issues between GNU and BSD userland used for testing.
• Added FreeBSD and MacOS in github actions CI

Version 4.0.0

At last! Many fixes since -rc1:

• Improved container installation. Provide Docker files for debian and
  almalinux, Apptainer for debian and alpine.
• Many fixes to the SAM output format:
  • Fixed improper reverse complements with 0x10 flag
  • Proper header tags with tabs instead of spaces
  • Added @sq entries in header
  • Better testing of SAM output conformance
• Fix path quotes in Perl scripts
• Fix error in testing with GCC>10: the uniform distribution code has changed
  and breaks testing reproducibility. Use the uniform distribution from GCC10.
• show_align offsets maximum raised to 99 billion
• Fixed many compilation warnings and potential build errors with newer compilers

Find below the source code mummer-4.0.0.tar.gz and an Apptainer binary distribution mummer-alpine.sif.

Mummer 4.0.0 release candidate 1

In this release we modified the output of delta2vcf to be fully compliant with vcf4.2 specification, validated by vcf-validator from vcftools. We also rolled back some changes in mummerplot and removed extra gnuplot options that may be incompatible with gnuplot version 4 or 5. We performed additional validation of the nucmer output.

Known issues:

1. use of the --maxmatch option results in memory overflow on certain reference sequences that contain long stretches of homopolymers; we are still investigating this issue. For now please use --batch 1 instead of --maxmatch, if --maxmatch fails, this will use seeds that may repeat between different reference sequences, but not within the same input sequence.

Mummer 4.0.0.beta5

This release fixed bug in mummerplot that prevented it from running on some systems, fixes bug in nucmer that resulted in valid alignments of large stretches of N's, and fixed missing install-sh. Release tested with make distcheck and unit testing.

MUMmer 4.0.0.beta3

In this release we disabled openMP in suffix array construction because it was causing system errors when user ran multiple nucmer processes in the same shell. We also added delta2vcf script:

delta2vcf < file.delta > file.vcf

The script converts delta file to a vcf file, detailing all substitutions and indels in the reference sequence with respect to the query sequence. This is useful for comparing two different assemblies of the same organism, assemblies of two different individuals from the same spcies, and looking for haplotype differences in haplotype resolved assemblies.

v4.0.0.beta2

• Moved to Artistic license 2 (from Artistic license 1)
• More compliant SAM output
• Install mummer.pc
• Work around bug that resulted in invalid delta file (negative match coordinate in query)

Download the source code mummer-4.0.0beta2.tar.gz.

Version 4.0.0beta1

• gnuplot/mummerplot fixes
• compilation on Mac
• fixed use of seeds in testing

Version 4.0 beta

v4.0.0beta

v4.0beta

Version 3.9.4alpha

• Parallelization of the suffix array LCP construction
• Query sequences optional if --save is used with nucmer
• Fix compilation issues with newer version of gcc & clang
• Speed improvement in delta-filter if filtering only by identity and/or length

Version 3.9.3alpha

• Fixed segfault and logical bug in save/load of index
• Better unit testing of suffix array