From bd1541dce1d99e28a30b6aa5ccc2391201df8a8e Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 7 Aug 2017 13:26:25 -0400
Subject: [PATCH] renamed simulation-related scripts

---
 misc/README.md                      | 10 +++-------
 misc/{pbsim-eval.js => sim-eval.js} |  0
 misc/{mason2fq.js => sim-mason2.js} |  0
 misc/{pbsim2fa.js => sim-pbsim.js}  |  0
 4 files changed, 3 insertions(+), 7 deletions(-)
 rename misc/{pbsim-eval.js => sim-eval.js} (100%)
 rename misc/{mason2fq.js => sim-mason2.js} (100%)
 rename misc/{pbsim2fa.js => sim-pbsim.js} (100%)

diff --git a/misc/README.md b/misc/README.md
index bfb76f6..c6e3371 100644
--- a/misc/README.md
+++ b/misc/README.md
@@ -13,16 +13,12 @@ page][k8bin].
   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
+* [sim-pbsim.js](sim-pbsim.js): convert reads simulated with [PBSIM][pbsim] to
   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 convert to PAF first:
-  ```sh
-  k8 sam2paf.js -p aln.sam | k8 pbsim-eval.js /dev/stdin
-  ```
+* [sim-eval.js](sim-eval.js): evaluate mapping accuracy for FASTA generated
+  with [sim-pbsim.js](sim-pbsim.js) or [sim-mason2.js](sim-mason2.js).
 
 * [sam2paf.js](sam2paf.js): convert SAM to PAF.
 
diff --git a/misc/pbsim-eval.js b/misc/sim-eval.js
similarity index 100%
rename from misc/pbsim-eval.js
rename to misc/sim-eval.js
diff --git a/misc/mason2fq.js b/misc/sim-mason2.js
similarity index 100%
rename from misc/mason2fq.js
rename to misc/sim-mason2.js
diff --git a/misc/pbsim2fa.js b/misc/sim-pbsim.js
similarity index 100%
rename from misc/pbsim2fa.js
rename to misc/sim-pbsim.js