Sat Oct 28 20:35:44 2023 UTC ()
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


(bacon)
diff -r1.1 -r1.2 pkgsrc/biology/fastq-trim/DESCR
diff -r1.3 -r1.4 pkgsrc/biology/fastq-trim/Makefile
diff -r1.2 -r1.3 pkgsrc/biology/fastq-trim/PLIST
diff -r1.2 -r1.3 pkgsrc/biology/fastq-trim/distinfo
cvs diff -r1.1 -r1.2 pkgsrc/biology/fastq-trim/DESCR (expand / switch to unified diff)

--- pkgsrc/biology/fastq-trim/DESCR 2022/11/06 22:49:37 1.1
+++ pkgsrc/biology/fastq-trim/DESCR 2023/10/28 20:35:44 1.2
@@ -1,5 +1,6 @@ @@ -1,5 +1,6 @@
1Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads 1Fastq-trim is a lightening fast read trimming tool for QA of DNA
2prior to analyses such as RNA-Seq. it runs in a fraction of the time required 2and RNA reads prior to analyses such as RNA-Seq. it runs in a
3by popular trimmers and uses only a few megabytes of RAM, so it will run 3fraction of the time required by popular trimmers and uses only a
4almost entirely in cache. The design supports adding any number of alignment 4few megabytes of RAM, so it will run almost entirely in cache.
5functions, so it can be easily adapted to any trimming needs. 5The design supports adding any number of alignment functions, so
 6it can be easily adapted to any trimming needs.
cvs diff -r1.3 -r1.4 pkgsrc/biology/fastq-trim/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/fastq-trim/Makefile 2022/12/28 15:27:16 1.3
+++ pkgsrc/biology/fastq-trim/Makefile 2023/10/28 20:35:44 1.4
@@ -1,16 +1,16 @@ @@ -1,16 +1,16 @@
1# $NetBSD: Makefile,v 1.3 2022/12/28 15:27:16 bacon Exp $ 1# $NetBSD: Makefile,v 1.4 2023/10/28 20:35:44 bacon Exp $
2 2
3DISTNAME= fastq-trim-0.1.2 3DISTNAME= fastq-trim-0.1.3
4CATEGORIES= biology 4CATEGORIES= biology
5MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/} 5MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
6 6
7OWNER= bacon@NetBSD.org 7OWNER= bacon@NetBSD.org
8HOMEPAGE= https://github.com/outpaddling/Fastq-trim 8HOMEPAGE= https://github.com/outpaddling/Fastq-trim
9COMMENT= Lightening fast sequence read trimmer 9COMMENT= Lightening fast sequence read trimmer
10LICENSE= 2-clause-bsd 10LICENSE= 2-clause-bsd
11 11
12MAKE_ENV= VERSION=${PKGVERSION} 12MAKE_ENV= VERSION=${PKGVERSION}
13 13
14LDFLAGS.SunOS= -lresolv 14LDFLAGS.SunOS= -lresolv
15 15
16pre-build: 16pre-build:
cvs diff -r1.2 -r1.3 pkgsrc/biology/fastq-trim/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/fastq-trim/PLIST 2022/12/11 21:25:47 1.2
+++ pkgsrc/biology/fastq-trim/PLIST 2023/10/28 20:35:44 1.3
@@ -1,14 +1,14 @@ @@ -1,14 +1,14 @@
1@comment $NetBSD: PLIST,v 1.2 2022/12/11 21:25:47 bacon Exp $ 1@comment $NetBSD: PLIST,v 1.3 2023/10/28 20:35:44 bacon Exp $
2bin/fastq-scum 2bin/fastq-scum
3bin/fastq-trim 3bin/fastq-trim
4include/fastq-trim-accessors.h 4include/fastq-trim-accessors.h
5include/fastq-trim-mutators.h 5include/fastq-trim-mutators.h
6include/fastq-trim-rvs.h 6include/fastq-trim-rvs.h
7include/fastq-trim.h 7include/fastq-trim.h
8lib/libfastq-trim.a 8lib/libfastq-trim.a
9man/man1/fastq-scum.1 9man/man1/fastq-scum.1
10man/man1/fastq-trim.1 10man/man1/fastq-trim.1
11man/man3/FASTQ_TRIM_ADAPTER1.3 11man/man3/FASTQ_TRIM_ADAPTER1.3
12man/man3/FASTQ_TRIM_ADAPTER1_AE.3 12man/man3/FASTQ_TRIM_ADAPTER1_AE.3
13man/man3/FASTQ_TRIM_ADAPTER2.3 13man/man3/FASTQ_TRIM_ADAPTER2.3
14man/man3/FASTQ_TRIM_ADAPTER2_AE.3 14man/man3/FASTQ_TRIM_ADAPTER2_AE.3
cvs diff -r1.2 -r1.3 pkgsrc/biology/fastq-trim/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/fastq-trim/distinfo 2022/12/11 21:25:47 1.2
+++ pkgsrc/biology/fastq-trim/distinfo 2023/10/28 20:35:44 1.3
@@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
1$NetBSD: distinfo,v 1.2 2022/12/11 21:25:47 bacon Exp $ 1$NetBSD: distinfo,v 1.3 2023/10/28 20:35:44 bacon Exp $
2 2
3BLAKE2s (fastq-trim-0.1.2.tar.gz) = d86b5a4a59c9b3e82b4a303c272e9818a9b54532e64d7e42e4c89dea34591fc4 3BLAKE2s (fastq-trim-0.1.3.tar.gz) = f346e25b1c5d14a532e2611a1a6f3d6c9fef4454e0848f1adbe70e0ee5ee76b2
4SHA512 (fastq-trim-0.1.2.tar.gz) = e27852410cc0af06e30d06e1266be6639ff2f63cd35c61801817b37241a6feb41ef5efc5e8668333a19d575a7c018a85113b3e6ec618e2fcbdb2572c05be6148 4SHA512 (fastq-trim-0.1.3.tar.gz) = 7fa94c7f4a97956fef98dbdd233b7628d1a49440fc8ba8e52e06e8e87343555ed325c4361f93865ad82863274018d625397d4b288d096196412865a22a106beb
5Size (fastq-trim-0.1.2.tar.gz) = 29796 bytes 5Size (fastq-trim-0.1.3.tar.gz) = 30596 bytes