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wrong sentence in README-alt
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lh3 committed Dec 11, 2014
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16 changes: 14 additions & 2 deletions NEWS.md
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Expand Up @@ -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)


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3 changes: 1 addition & 2 deletions README-alt.md
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Expand Up @@ -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
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