Michael R. Crusoe pushed to branch upstream at Debian Med / bwa-mem2
Commits: d40c35ba by Michael R. Crusoe at 2021-11-18T18:55:27+01:00 New upstream version 2.2.1 - - - - - 4 changed files: - NEWS.md - README.md - src/fastmap.cpp - src/main.cpp Changes: ===================================== NEWS.md ===================================== @@ -1,3 +1,32 @@ +Release 2.2.1 (17 March 2021) +--------------------------------- +Hotfix for v2.2: Fixed the bug mentioned in #135. + + +Release 2.2 (8 March 2021) +--------------------------------- +Changes since the last release (2.1): + +* Passed the validation test on ~88 billions reads (Credits: Keiran Raine, CASM division, Sanger Institute) +* Fixed bugs reported in #109 causing mismatch between bwa-mem and bwa-mem2 +* Fixed the issue (# 112) causing crash due to corrupted thread id +* Using all the SSE flags to create optimized SSE41 and SSE42 binaries + + +Release 2.1 (16 October 2020) +--------------------------------- +Release 2.1 of BWA-MEM2. + +Changes since the last release (2.0): +* *Smaller index*: the index size on disk is down by 8 times and in memory by 4 times due to moving to only one type of FM-index (2bit.64 instead of 2bit.64 and 8bit.32) and 8x compression of suffix array. For example, for human genome, index size on disk is down to ~10GB from ~80GB and memory footprint is down to ~10GB from ~40GB. There is a substantial decrease in index IO time due to the reduction and hardly any performance impact on read mapping. + +* Added support for 2 more execution modes: sse4.2 and avx. + +* Fixed multiple bugs including those reported in Issues #71, #80 and #85. + +* Merged multiple pull requests. + + Release 2.0 (9 July 2020) --------------------------------- This is the first production release of BWA-MEM2. ===================================== README.md ===================================== @@ -51,10 +51,10 @@ For general users, it is recommended to use the precompiled binaries from the runs faster than gcc-compiled binaries. The precompiled binaries also indirectly support CPU dispatch. The `bwa-mem2` binary can automatically choose the most efficient implementation based on the SIMD instruction set available -on the running machine. Precompiled binaries were generated on a CentOS6 +on the running machine. Precompiled binaries were generated on a CentOS7 machine using the following command line: ```sh -make CXX=icpc +make CXX=icpc multi ``` [bwa]: https://github.com/lh3/bwa ===================================== src/fastmap.cpp ===================================== @@ -953,6 +953,7 @@ int main_mem(int argc, char *argv[]) tprof[PROCESS][0] += __rdtsc() - tim; // free memory + int32_t nt = aux.opt->n_threads; _mm_free(ref_string); free(hdr_line); free(opt); @@ -974,7 +975,7 @@ int main_mem(int argc, char *argv[]) /* Display runtime profiling stats */ tprof[MEM][0] = __rdtsc() - tprof[MEM][0]; - display_stats(aux.opt->n_threads); + display_stats(nt); return 0; } ===================================== src/main.cpp ===================================== @@ -32,7 +32,7 @@ Contacts: Vasimuddin Md <[email protected]>; Sanchit Misra <sanchit.misra@ #include "main.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "2.2" +#define PACKAGE_VERSION "2.2.1" #endif View it on GitLab: https://salsa.debian.org/med-team/bwa-mem2/-/commit/d40c35baefeef0b6a49219db6362692b104cc71b -- View it on GitLab: https://salsa.debian.org/med-team/bwa-mem2/-/commit/d40c35baefeef0b6a49219db6362692b104cc71b You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
