From efa0dd561aae19fb988dd2e5069fec1cf7f415e3 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 10 Dec 2014 23:20:46 -0500 Subject: [PATCH] wrong sentence in README-alt --- NEWS.md | 16 ++++++++++++++-- README-alt.md | 3 +-- 2 files changed, 15 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index 4cf69ab..4219e94 100644 --- a/NEWS.md +++ b/NEWS.md @@ -27,11 +27,23 @@ Other notable changes to BWA-MEM: finding the best hit, not all hits. Option `-x pbread` is still available, but hidden on the command line. - * Added new pre-setting for Oxford Nanopore 2D reads. For small genomes, - though, LAST is still more sensitive. + * Added a new pre-setting for Oxford Nanopore 2D reads. LAST is still a little + more sensitive on bacterial data, but bwa-mem is times faster on human data. * Added LAST-like seeding. This improves the accuracy for longer reads. + * Added option `-H` to insert arbitrary header lines. + + * Smarter option `-p`. Given an interleaved FASTQ stream, old bwa-mem identifies + the 2i-th and (2i+1)-th reads as a read pair. The new verion identifies + adjacent reads with the same read name as a read pair. It is possible to mix + single-end and paired-end reads in one FASTQ. + + * Improved parallelization. Old bwa-mem waits for I/O. The new version puts + I/O on a separate thread. It performs mapping while reading FASTQ and + writing SAM. This saves significant wall-clock time when reading from + or writing to a slow Unix pipe. + (0.7.11: XX November 2014, rXXX) diff --git a/README-alt.md b/README-alt.md index 088be47..0d97ffd 100644 --- a/README-alt.md +++ b/README-alt.md @@ -58,8 +58,7 @@ alignments and assigns mapQ following these two rules: 2. If there are no non-ALT hits, the best ALT hit is outputted as the primary alignment. If there are both ALT and non-ALT hits, non-ALT hits will be - primary and ALT hits be supplementary (SAM flag 0x800) if ALT hits are better - than the best overlapping non-ALT hits. + primary and ALT hits be supplementary (SAM flag 0x800). In theory, non-ALT alignments from step 1 should be identical to alignments against the reference genome with ALT contigs. In practice, the two types of