From 756379bf831a3dcf04b2e8d98eb10363c0ddaf0f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 2 Feb 2018 14:43:58 -0500
Subject: [PATCH] Documented paf2diff.js (more to come later)

---
 misc/README.md   | 14 ++++++++++++--
 misc/paf2diff.js |  2 ++
 2 files changed, 14 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 misc/paf2diff.js

diff --git a/misc/README.md b/misc/README.md
index 067738a..d3eecd4 100644
--- a/misc/README.md
+++ b/misc/README.md
@@ -12,11 +12,13 @@ minimap2 -cx splice ref.fa rna-seq.fq | splice2bed.js -   # convert splice aln t
 
 - [Getting Started](#started)
 - [Introduction](#intro)
-- [Use Cases](#usage)
+- [Calling Variants from Assemblies](#asmvar)
+- [Format Conversion](#conv)
   - [Convert PAF to other formats](#paf2aln)
   - [Convert SAM to PAF](#sam2paf)
   - [Convert GTF/GFF3 to BED12 format](#gff2bed)
   - [Convert spliced alignment to BED12](#splice2bed)
+- [Evaluation](#eval)
   - [Evaluating mapping accuracy with simulated reads](#mapeval)
   - [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
 `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
 
@@ -55,6 +63,8 @@ seamlessly works with both GTF and GFF3.
 Script [splice2bed.js](splice2bed.js) converts spliced alignment in SAM or PAF
 to 12-column BED format.
 
+## <a name="eval"></a>Evaluation
+
 ### <a name="mapeval"></a>Evaluating mapping accuracy with simulated reads
 
 Script [sim-pbsim.js](sim-pbsim.js) converts the MAF output of [pbsim][pbsim]
diff --git a/misc/paf2diff.js b/misc/paf2diff.js
old mode 100644
new mode 100755
index 30fdd28..7aeef9a
--- a/misc/paf2diff.js
+++ b/misc/paf2diff.js
@@ -1,3 +1,5 @@
+#!/usr/bin/env k8
+
 var getopt = function(args, ostr) {
 	var oli; // option letter list index
 	if (typeof(getopt.place) == 'undefined')