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Documented paf2diff.js (more to come later)

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Heng Li 2018-02-02 14:43:58 -05:00
parent 41fd8a966a
commit 756379bf83
2 changed files with 14 additions and 2 deletions
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14
misc/README.md
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@ -12,11 +12,13 @@ minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js - # convert splice aln t
- [Getting Started](#started) - [Getting Started](#started)
- [Introduction](#intro) - [Introduction](#intro)
- [Use Cases](#usage) - [Calling Variants from Assemblies](#asmvar)
- [Format Conversion](#conv)
- [Convert PAF to other formats](#paf2aln) - [Convert PAF to other formats](#paf2aln)
- [Convert SAM to PAF](#sam2paf) - [Convert SAM to PAF](#sam2paf)
- [Convert GTF/GFF3 to BED12 format](#gff2bed) - [Convert GTF/GFF3 to BED12 format](#gff2bed)
- [Convert spliced alignment to BED12](#splice2bed) - [Convert spliced alignment to BED12](#splice2bed)
- [Evaluation](#eval)
- [Evaluating mapping accuracy with simulated reads](#mapeval) - [Evaluating mapping accuracy with simulated reads](#mapeval)
- [Evaluating read overlap sensitivity](#oveval) - [Evaluating read overlap sensitivity](#oveval)
@ -33,7 +35,13 @@ cp k8-0.2.4/k8-`uname -s` k8
It is highly recommended to copy the executable `k8` to a directory on your It is highly recommended to copy the executable `k8` to a directory on your
`PATH` such as `/usr/bin/env` can find it. `PATH` such as `/usr/bin/env` can find it.
## <a name="usage"></a>Use Cases ## <a name="asmvar"></a>Calling Variants from Assemblies
Script [paf2diff.js](paf2diff.js) calls variants from coordinate-sorted
assembly-to-reference alignment having the [cs tag][cs] (requiring the `--cs`
minimap2 option).
## <a name="conv"></a>Format Conversion
### <a name="paf2aln"></a>Convert PAF to other formats ### <a name="paf2aln"></a>Convert PAF to other formats
@ -55,6 +63,8 @@ seamlessly works with both GTF and GFF3.
Script [splice2bed.js](splice2bed.js) converts spliced alignment in SAM or PAF Script [splice2bed.js](splice2bed.js) converts spliced alignment in SAM or PAF
to 12-column BED format. to 12-column BED format.
## <a name="eval"></a>Evaluation
### <a name="mapeval"></a>Evaluating mapping accuracy with simulated reads ### <a name="mapeval"></a>Evaluating mapping accuracy with simulated reads
Script [sim-pbsim.js](sim-pbsim.js) converts the MAF output of [pbsim][pbsim] Script [sim-pbsim.js](sim-pbsim.js) converts the MAF output of [pbsim][pbsim]

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misc/paf2diff.js 100644 → 100755
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@ -1,3 +1,5 @@
#!/usr/bin/env k8
var getopt = function(args, ostr) { var getopt = function(args, ostr) {
var oli; // option letter list index var oli; // option letter list index
if (typeof(getopt.place) == 'undefined') if (typeof(getopt.place) == 'undefined')