CVS commit: pkgsrc/biology/fastq-trim

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Oct 28 20:35:44 UTC 2023

Modified Files:
        pkgsrc/biology/fastq-trim: DESCR Makefile PLIST distinfo

Log Message:
biology/fastq-trim: Update to 0.1.3

fastq-scum: Add zstd and lz4 support
Add low_qual_base_count update for paired end reads
Clean up and expand final output format
A few other minor improvements
Updates for latest libxtend API
Improvements to test script

Changes: https://github.com/auerlab/fastq-trim/releases


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/fastq-trim/DESCR
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/fastq-trim/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/fastq-trim/PLIST \
    pkgsrc/biology/fastq-trim/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/fastq-trim/DESCR
diff -u pkgsrc/biology/fastq-trim/DESCR:1.1 pkgsrc/biology/fastq-trim/DESCR:1.2
--- pkgsrc/biology/fastq-trim/DESCR:1.1 Sun Nov  6 22:49:37 2022
+++ pkgsrc/biology/fastq-trim/DESCR     Sat Oct 28 20:35:44 2023
@@ -1,5 +1,6 @@
-Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads
-prior to analyses such as RNA-Seq.  it runs in a fraction of the time required
-by popular trimmers and uses only a few megabytes of RAM, so it will run
-almost entirely in cache.  The design supports adding any number of alignment
-functions, so it can be easily adapted to any trimming needs.
+Fastq-trim is a lightening fast read trimming tool for QA of DNA
+and RNA reads prior to analyses such as RNA-Seq.  it runs in a
+fraction of the time required by popular trimmers and uses only a
+few megabytes of RAM, so it will run almost entirely in cache.
+The design supports adding any number of alignment functions, so
+it can be easily adapted to any trimming needs.

Index: pkgsrc/biology/fastq-trim/Makefile
diff -u pkgsrc/biology/fastq-trim/Makefile:1.3 pkgsrc/biology/fastq-trim/Makefile:1.4
--- pkgsrc/biology/fastq-trim/Makefile:1.3      Wed Dec 28 15:27:16 2022
+++ pkgsrc/biology/fastq-trim/Makefile  Sat Oct 28 20:35:44 2023
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.3 2022/12/28 15:27:16 bacon Exp $
+# $NetBSD: Makefile,v 1.4 2023/10/28 20:35:44 bacon Exp $
 
-DISTNAME=      fastq-trim-0.1.2
+DISTNAME=      fastq-trim-0.1.3
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=outpaddling/}
 

Index: pkgsrc/biology/fastq-trim/PLIST
diff -u pkgsrc/biology/fastq-trim/PLIST:1.2 pkgsrc/biology/fastq-trim/PLIST:1.3
--- pkgsrc/biology/fastq-trim/PLIST:1.2 Sun Dec 11 21:25:47 2022
+++ pkgsrc/biology/fastq-trim/PLIST     Sat Oct 28 20:35:44 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2022/12/11 21:25:47 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2023/10/28 20:35:44 bacon Exp $
 bin/fastq-scum
 bin/fastq-trim
 include/fastq-trim-accessors.h
Index: pkgsrc/biology/fastq-trim/distinfo
diff -u pkgsrc/biology/fastq-trim/distinfo:1.2 pkgsrc/biology/fastq-trim/distinfo:1.3
--- pkgsrc/biology/fastq-trim/distinfo:1.2      Sun Dec 11 21:25:47 2022
+++ pkgsrc/biology/fastq-trim/distinfo  Sat Oct 28 20:35:44 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.2 2022/12/11 21:25:47 bacon Exp $
+$NetBSD: distinfo,v 1.3 2023/10/28 20:35:44 bacon Exp $
 
-BLAKE2s (fastq-trim-0.1.2.tar.gz) = d86b5a4a59c9b3e82b4a303c272e9818a9b54532e64d7e42e4c89dea34591fc4
-SHA512 (fastq-trim-0.1.2.tar.gz) = e27852410cc0af06e30d06e1266be6639ff2f63cd35c61801817b37241a6feb41ef5efc5e8668333a19d575a7c018a85113b3e6ec618e2fcbdb2572c05be6148
-Size (fastq-trim-0.1.2.tar.gz) = 29796 bytes
+BLAKE2s (fastq-trim-0.1.3.tar.gz) = f346e25b1c5d14a532e2611a1a6f3d6c9fef4454e0848f1adbe70e0ee5ee76b2
+SHA512 (fastq-trim-0.1.3.tar.gz) = 7fa94c7f4a97956fef98dbdd233b7628d1a49440fc8ba8e52e06e8e87343555ed325c4361f93865ad82863274018d625397d4b288d096196412865a22a106beb
+Size (fastq-trim-0.1.3.tar.gz) = 30596 bytes