[pkgsrc/trunk]: pkgsrc/biology/fastq-trim biology/fastq-trim: Lightening fast...

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/d2c38071ea06
branches:  trunk
changeset: 387792:d2c38071ea06
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Sun Nov 06 22:49:37 2022 +0000

description:
biology/fastq-trim: Lightening fast sequence read trimmer

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.

diffstat:

 biology/fastq-trim/DESCR    |   5 ++
 biology/fastq-trim/Makefile |  21 ++++++++++++
 biology/fastq-trim/PLIST    |  76 +++++++++++++++++++++++++++++++++++++++++++++
 biology/fastq-trim/distinfo |   5 ++
 4 files changed, 107 insertions(+), 0 deletions(-)

diffs (123 lines):

diff -r ee94e3bd9104 -r d2c38071ea06 biology/fastq-trim/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fastq-trim/DESCR  Sun Nov 06 22:49:37 2022 +0000
@@ -0,0 +1,5 @@
+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.
diff -r ee94e3bd9104 -r d2c38071ea06 biology/fastq-trim/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fastq-trim/Makefile       Sun Nov 06 22:49:37 2022 +0000
@@ -0,0 +1,21 @@
+# $NetBSD: Makefile,v 1.1 2022/11/06 22:49:37 bacon Exp $
+
+DISTNAME=      fastq-trim-0.1.1.16
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=outpaddling/}
+GITHUB_TAG=    58a016f250a9b785bfed574ce471ec7e23cdaa4a
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      https://github.com/outpaddling/Fastq-trim
+COMMENT=       Lightening fast sequence read trimmer
+LICENSE=       2-clause-bsd
+
+MAKE_ENV=      VERSION=${PKGVERSION}
+
+LDFLAGS.SunOS= -lresolv
+
+pre-build:
+       (cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend)
+
+.include "../../biology/biolibc/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff -r ee94e3bd9104 -r d2c38071ea06 biology/fastq-trim/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fastq-trim/PLIST  Sun Nov 06 22:49:37 2022 +0000
@@ -0,0 +1,76 @@
+@comment $NetBSD: PLIST,v 1.1 2022/11/06 22:49:37 bacon Exp $
+bin/fastq-scum
+bin/fastq-trim
+include/fastq-trim-accessors.h
+include/fastq-trim-mutators.h
+include/fastq-trim-rvs.h
+include/fastq-trim.h
+lib/libfastq-trim.a
+man/man1/fastq-scum.1
+man/man1/fastq-trim.1
+man/man3/FASTQ_TRIM_ADAPTER1.3
+man/man3/FASTQ_TRIM_ADAPTER1_AE.3
+man/man3/FASTQ_TRIM_ADAPTER2.3
+man/man3/FASTQ_TRIM_ADAPTER2_AE.3
+man/man3/FASTQ_TRIM_ADAPTER_MATCH_FUNCTION.3
+man/man3/FASTQ_TRIM_INFILE1.3
+man/man3/FASTQ_TRIM_INFILE1_AE.3
+man/man3/FASTQ_TRIM_INFILE2.3
+man/man3/FASTQ_TRIM_INFILE2_AE.3
+man/man3/FASTQ_TRIM_INSTREAM1.3
+man/man3/FASTQ_TRIM_INSTREAM1_AE.3
+man/man3/FASTQ_TRIM_INSTREAM2.3
+man/man3/FASTQ_TRIM_INSTREAM2_AE.3
+man/man3/FASTQ_TRIM_MAX_MISMATCH_PERCENT.3
+man/man3/FASTQ_TRIM_MIN_LENGTH.3
+man/man3/FASTQ_TRIM_MIN_MATCH.3
+man/man3/FASTQ_TRIM_MIN_QUAL.3
+man/man3/FASTQ_TRIM_OUTFILE1.3
+man/man3/FASTQ_TRIM_OUTFILE1_AE.3
+man/man3/FASTQ_TRIM_OUTFILE2.3
+man/man3/FASTQ_TRIM_OUTFILE2_AE.3
+man/man3/FASTQ_TRIM_OUTSTREAM1.3
+man/man3/FASTQ_TRIM_OUTSTREAM1_AE.3
+man/man3/FASTQ_TRIM_OUTSTREAM2.3
+man/man3/FASTQ_TRIM_OUTSTREAM2_AE.3
+man/man3/FASTQ_TRIM_PHRED_BASE.3
+man/man3/FASTQ_TRIM_POLYA_MIN_LEN.3
+man/man3/FASTQ_TRIM_VERBOSE.3
+man/man3/fastq_trim_set_adapter1.3
+man/man3/fastq_trim_set_adapter1_ae.3
+man/man3/fastq_trim_set_adapter1_cpy.3
+man/man3/fastq_trim_set_adapter2.3
+man/man3/fastq_trim_set_adapter2_ae.3
+man/man3/fastq_trim_set_adapter2_cpy.3
+man/man3/fastq_trim_set_adapter_match_function.3
+man/man3/fastq_trim_set_infile1.3
+man/man3/fastq_trim_set_infile1_ae.3
+man/man3/fastq_trim_set_infile1_cpy.3
+man/man3/fastq_trim_set_infile2.3
+man/man3/fastq_trim_set_infile2_ae.3
+man/man3/fastq_trim_set_infile2_cpy.3
+man/man3/fastq_trim_set_instream1.3
+man/man3/fastq_trim_set_instream1_ae.3
+man/man3/fastq_trim_set_instream1_cpy.3
+man/man3/fastq_trim_set_instream2.3
+man/man3/fastq_trim_set_instream2_ae.3
+man/man3/fastq_trim_set_instream2_cpy.3
+man/man3/fastq_trim_set_max_mismatch_percent.3
+man/man3/fastq_trim_set_min_length.3
+man/man3/fastq_trim_set_min_match.3
+man/man3/fastq_trim_set_min_qual.3
+man/man3/fastq_trim_set_outfile1.3
+man/man3/fastq_trim_set_outfile1_ae.3
+man/man3/fastq_trim_set_outfile1_cpy.3
+man/man3/fastq_trim_set_outfile2.3
+man/man3/fastq_trim_set_outfile2_ae.3
+man/man3/fastq_trim_set_outfile2_cpy.3
+man/man3/fastq_trim_set_outstream1.3
+man/man3/fastq_trim_set_outstream1_ae.3
+man/man3/fastq_trim_set_outstream1_cpy.3
+man/man3/fastq_trim_set_outstream2.3
+man/man3/fastq_trim_set_outstream2_ae.3
+man/man3/fastq_trim_set_outstream2_cpy.3
+man/man3/fastq_trim_set_phred_base.3
+man/man3/fastq_trim_set_polya_min_len.3
+man/man3/fastq_trim_set_verbose.3
diff -r ee94e3bd9104 -r d2c38071ea06 biology/fastq-trim/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/fastq-trim/distinfo       Sun Nov 06 22:49:37 2022 +0000
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2022/11/06 22:49:37 bacon Exp $
+
+BLAKE2s (fastq-trim-0.1.1.16-58a016f250a9b785bfed574ce471ec7e23cdaa4a.tar.gz) = a2383eed63d5bb75dbb8c1ca2f6a5f08f737cb6243772e87d0477938cc3440f7
+SHA512 (fastq-trim-0.1.1.16-58a016f250a9b785bfed574ce471ec7e23cdaa4a.tar.gz) = 
26d0bf350bac6b3bbfb98d35e6587a1b58a9f353f376f676d97a9c6ff36e41ea05a906eeee2089834f05e26121b7014fd93ef5ba732eb8f8d977edfacaa01225
+Size (fastq-trim-0.1.1.16-58a016f250a9b785bfed574ce471ec7e23cdaa4a.tar.gz) = 29819 bytes