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minor clarification

This commit is contained in:
Heng Li 2017-08-04 14:49:25 -04:00
parent 890d7bbd5b
commit 269b8661b9
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misc/README.md
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The [K8 Javascript engine][k8] is needed to run Javascripts in this directory.
The [K8 Javascript shell][k8] is needed to run Javascripts in this directory.
Precompiled k8 binaries for Mac and Linux can be found at the [K8 release
page][k8].
* [paf2aln.js](paf2aln.js): convert PAF to [MAF][maf] or BLAST-like output for
eyeballing. PAF has to be generated with minimap2 option `-S`.
eyeballing. PAF has to be generated with minimap2 option `-S`, which writes
the aligned sequences to the `cs` tag.
* [mapstat.js](mapstat.js): output basic statistics such as the number of
non-redundant mapped bases, number of split and secondary alignments and
number of long gaps. This scripts seamlessly works with both SAM and PAF.
* [pbsim2fa.js](pbsim2fa.js): convert reads simulated with [PBSIM][pbsim] to
FASTA and encode the true mapping positions to read names.
FASTA and encode the true mapping positions to read names in a format like
`S1_33!chr1!225258409!225267761!-`.
* [pbsim-eval.js](pbsim-eval.js): evaluate mapping accuracy for FASTA generated
with [pbsim2fa.js](pbsim2fa.js). This script only works with PAF. For SAM,
please run the following instead:
please convert to PAF first:
```sh
k8 sam2paf.js -p aln.sam | k8 pbsim-eval.js /dev/stdin
```