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Merge branch 'dev'

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Heng Li 2014-12-10 23:21:13 -05:00
parent 9649f3496f efa0dd561a
commit 139df93af9
2 changed files with 15 additions and 4 deletions
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16
NEWS.md
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@ -27,11 +27,23 @@ Other notable changes to BWA-MEM:
finding the best hit, not all hits. Option `-x pbread` is still available, finding the best hit, not all hits. Option `-x pbread` is still available,
but hidden on the command line. but hidden on the command line.
* Added new pre-setting for Oxford Nanopore 2D reads. For small genomes, * Added a new pre-setting for Oxford Nanopore 2D reads. LAST is still a little
though, LAST is still more sensitive. 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 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) (0.7.11: XX November 2014, rXXX)

3
README-alt.md
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@ -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 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 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 primary and ALT hits be supplementary (SAM flag 0x800).
than the best overlapping non-ALT hits.
In theory, non-ALT alignments from step 1 should be identical to alignments 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 against the reference genome with ALT contigs. In practice, the two types of