ShoRAH 2 (pre-relase)

This is a pre-release version of ShoRAH 2.

It can be considered suitable for production

• it fixes Long deletions

Caution:

Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognize Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.99.3.tar.bz2) or xzipped (shorah-1.99.3.tar.xz).

ShoRAH 2 (pre-release)

This is a pre-release version of ShoRAH 2.

It can be considered suitable for production

• fixes crashes introduced by version 1.10 of HTSlib
• supports cram files
• updates in documentation and tests

Caution:

Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognize Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.99.2.tar.bz2) or xzipped (shorah-1.99.2.tar.xz).

update 2020-08-15 Small cosmetic change, the previous tarball showed the wrong version number. There is no change in the source code itself.

ShoRAH 2 (pre-release)

This is a pre-release version of ShoRAH 2, which is used by V-pipe in the current sars-cov-2 sequencing efforts, it is also used in doi:10.1101/2020.06.09.142919.

It can be considered suitable for production

• fixes duplicate counts of very highly abundant haplotypes (was causing posterior > 1.0).
• fixes crashes due to unhandled exp underflow exceptions.
• fixes issues with missing .version file (issue #72 and #76)
• gives an option (-t/--threads) to limit thread count.
• gives an option (- p/--threshold) to change posterior threshold when calling SNVs.

Caution:

Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognize Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.99.1.tar.bz2) or xzipped (shorah-1.99.1.tar.xz).

ShoRAH 2 (meson-less pre-release)

This is a pre-release version of ShoRAH 2

It can be considered suitable for production, but misses fully tested meson build.

• This pre-release merges the speed optimisations from the allocaholic branch
• This pre-release incorporates the support for VCF format output

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.99.0.tar.bz2) or xzipped (shorah-1.99.0.tar.xz).

Pre-release of ShoRAH version 2

This is a beta version of version 2 of ShoRAH, which was provided to the Geneva Genomics Platform for data processing of local haplotypes.

• This beta incorportates several fixes against issues that caused error and crashes due to regions with low and/or poor coverage.
• This beta also incorporates the speed optimisations from the allocaholic branch

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-genevagenomics_201909.tar.bz2) or xzipped.

update 20191030: fixed missing bootstraping

v1.9.95

This is a beta version of version 2 of ShoRAH.

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.9.95.tar.bz2).

Bugfix version: correct inconsistencies in snv calculation

A missing initialization in fil.cpp produced erroneous results in p-values of SNVs.

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.1.3.tar.bz2).

v1.1.2

All executables now return exit code 0 when queried with -h.

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.1.2.tar.bz2).

v1.1.1

Small Gzip-related handling bug in Python.

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.1.1.tar.bz2).

v1.1.0

Python scripts are now compatible with Python 2 and 3, with 3 being preferred. The C++ code has received a number of performance improvements (using POPCNT intrinsics).

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.1.0.tar.bz2).