[med-svn] [Git][med-team/bwa-mem2][upstream] New upstream version 2.2.1

[Michael R. Crusoe (@crusoe)]

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 <vasimuddin.md at intel.com>; 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

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