piscem v0.7.0-beta

version 0.7.0-beta

piscem v0.6.3

Fixes a silly bug in the streaming iterator used for mapping that could sometimes cause a k-mer lookup to fail. Observed differences should be very small, but this fix can lead to more precise (i.e. better) mappings.

piscem v0.6.2

Expand fix from v0.6.1 to the alternative (non-shared minimizer) streaming query.

piscem v0.6.1

This release fixes a bug in streaming query that could, in rare circumstances, result in a segmentation fault (coming from the C++ piscem-cpp library). The corresponding issue was tracked here for those interested, and is resolved in this release.

piscem v0.6.0

This version fixes an issue in the streaming canonical query class that is used to speed up index search for streaming queries. There were specific variables tracking state that were not always properly reset. As a result, a small number of queries could return invalid results (usually causing the corresponding reads not to map). This commit addresses this issue. The effect was quite rare (occurring in ~0.01-0.02% of reads), but the streaming query results now always match the results one would get without using the streaming optimization.

piscem v0.5.1

This release fixes an issue related to the construction of the index on very small references (or with very small values of k and m) when the number of threads used for construction was set as a large number.

The specific fix limits the number of threads used in minimizer index construction (first step of sshash) to 8 (to match upstream sshash). This avoids some crashes observed when building the index on very small reference sets or with very small k / m.

piscem v0.5.0

piscem v0.5.0

piscem v0.4.3

piscem v0.4.3