From a458442b241dc70ed5223be36c8f5c8f0c057644 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 16 Sep 2014 14:38:41 -0400 Subject: [PATCH] r845: updated NEWS I will use the new version for a while and then release it. --- NEWS.md | 41 +++++++++++++++++++++++++++++++++++++++++ main.c | 2 +- 2 files changed, 42 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 33a47601..cc7946c6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,44 @@ +Release 0.7.11 (16 September, 2014) +----------------------------------- + +A major change to BWA-MEM is the support of mapping to ALT contigs. To use this +feature, users need to manually create a file ".alt" with each line +giving the name of an ALT contig. In mapping, BWA-MEM considers all chromosomes +and contigs equally when it finds seeds, constructs chains, extends seeds and +derives the final alignments. It also uses all hits for the estimation of +mapping quality of ALT hits. However, BWA-MEM ignores ALT hits when it +estimates the mapping quality of hits to the primary assembly. As a result, +having ALT contigs almost has not effect on alignments to the primary assembly +(seeding may be affected in rare corner cases). At the same time, users may +get a primary alignment to ALT contigs (no 0x800 flag) if there are no good +hits to the primary assembly, or get a supplementary alignment to ALT contigs +if it is better than hits to the primary assembly. Since this release, it is +recommended to include ALT contigs. + +Users may consider to use ALT contigs from GRCh38. I am also constructing a +non-redundant and more complete set of sequences missing from GRCh38. + +Other notable changes to BWA-MEM: + + * Added option `-b` to `bwa index`. This option tunes the batch size used in + the construction of BWT. It is advised to use large `-b` for huge reference + sequences such as the *nt* database. + + * Optimized for PacBio data. This includes a change to the scoring based on a + mini-study done by Aaron Quinlan and a heuristic speedup. Further speedup is + possible, but needs more careful investigation. + + * Dropped PacBio read-to-read alignment for now. BWA-MEM is only good at + finding the best hit, not all hits. Option `-x pbread` is still available, + but not shown on the command line. + + * Added new pre-setting for Oxford Nanopore 2D reads. For small genomes, + though, LAST is still more sensitive. + +(0.7.11: 16 September 2014, r845) + + + Release 0.7.10 (13 July, 2014) ------------------------------ diff --git a/main.c b/main.c index 903d4ce9..35e598b2 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r844-dirty" +#define PACKAGE_VERSION "0.7.10-r845-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);