[med-svn] [Git][med-team/adapterremoval][master] 5 commits: No patches needed in new upstream version any more
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Apr 15 14:52:12 BST 2022
Andreas Tille pushed to branch master at Debian Med / adapterremoval
Commits:
4369101d by Andreas Tille at 2022-04-15T15:43:50+02:00
No patches needed in new upstream version any more
- - - - -
dd439107 by Andreas Tille at 2022-04-15T15:44:08+02:00
New upstream version 2.3.3
- - - - -
cbf6d9c1 by Andreas Tille at 2022-04-15T15:44:08+02:00
routine-update: New upstream version
- - - - -
526ce929 by Andreas Tille at 2022-04-15T15:44:12+02:00
Update upstream source from tag 'upstream/2.3.3'
Update to upstream version '2.3.3'
with Debian dir 550f965c5f2b52c8f910e602234f9a6df5639b97
- - - - -
bc20bcb7 by Andreas Tille at 2022-04-15T15:46:15+02:00
routine-update: Ready to upload to unstable
- - - - -
12 changed files:
- AdapterRemoval.1
- CHANGES.md
- debian/changelog
- − debian/patches/2to3.patch
- − debian/patches/adapt-benchmarking.patch
- − debian/patches/delete_adapterremoval1x_completely.patch
- − debian/patches/reduce_benchmark_length.patch
- − debian/patches/series
- − debian/patches/update-catch2.patch
- docs/conf.py
- src/main.hpp
- tests/unit/catch.hpp
Changes:
=====================================
AdapterRemoval.1
=====================================
@@ -1,8 +1,5 @@
.\" Man page generated from reStructuredText.
.
-.TH "ADAPTERREMOVAL" "1" "Mar 17, 2021" "2.3.0" "AdapterRemoval"
-.SH NAME
-AdapterRemoval \- Fast short-read adapter trimming and processing
.
.nr rst2man-indent-level 0
.
@@ -30,6 +27,9 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
..
+.TH "ADAPTERREMOVAL" "1" "Apr 15, 2022" "2.3.3" "AdapterRemoval"
+.SH NAME
+AdapterRemoval \- Fast short-read adapter trimming and processing
.SH SYNOPSIS
.sp
\fBAdapterRemoval\fP [\fIoptions\fP\&...] \-\-file1 <\fIfilenames\fP> [\-\-file2 <\fIfilenames\fP>]
=====================================
CHANGES.md
=====================================
@@ -1,3 +1,7 @@
+### Version 2.3.3 - 2022-04-15
+
+ * Updated Catch2 to fix compilation with glibc 2.34, courtesy of loganrosen.
+
### Version 2.3.2 - 2021-03-17
* Improved error messages when AdapterRemoval failed to open or write FASTQ
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+adapterremoval (2.3.3-1) unstable; urgency=medium
+
+ * No patches needed in new upstream version any more
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Fri, 15 Apr 2022 15:44:21 +0200
+
adapterremoval (2.3.2-2) unstable; urgency=medium
[ Steve Langasek ]
=====================================
debian/patches/2to3.patch deleted
=====================================
@@ -1,321 +0,0 @@
-Description: Convert benchmark scripts from Python2 to Python3 using 2to3 even if not used in package
-Bug-Debian: https://bugs.debian.org/942927
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 15 Dec 2019 15:12:53 +0100
-Comment: Deactivated since benchmark script vanished
-
---- a/benchmark/benchmark.sh
-+++ b/benchmark/benchmark.sh
-@@ -194,7 +194,7 @@ function shuffle_and_run()
- echo > /dev/stderr
- echo "Shuffling batch ..." > /dev/stderr
-
-- python -c "import sys, random
-+ python3 -c "import sys, random
- lines = sys.stdin.readlines()
- random.shuffle(lines)
- sys.stdout.write(''.join(lines))" |
---- a/benchmark/scripts/evaluate.py
-+++ b/benchmark/scripts/evaluate.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- # -*- coding: utf-8 -*-
- # Copyright (c) 2014 Mikkel Schubert <MikkelSch at gmail.com>
- #
-@@ -131,10 +131,10 @@ class Summary(object):
- def missing_reads(expectations, se_mode):
- if se_mode:
- reads = [(key, [pair[0], None])
-- for key, pair in expectations.iteritems()
-+ for key, pair in expectations.items()
- if pair[0] is not None]
- else:
-- reads = [(key, pair) for key, pair in expectations.iteritems()
-+ reads = [(key, pair) for key, pair in expectations.items()
- if pair != [None, None]]
-
- max_errors = 0
-@@ -238,7 +238,7 @@ def evaluate(args, expectations, trimmed
- eval_func(args, expectations, stat, record)
-
- if args.dimers_are_discarded:
-- for key, pair in expectations.items():
-+ for key, pair in list(expectations.items()):
- if args.read_mode in ("SE", "MIXED_SE"):
- pair[1] = None
-
-@@ -313,7 +313,7 @@ def read_expected_lengths(args):
- results = collections.defaultdict(lambda: [None, None])
- for line in open_ro(args.read_info):
- if line.startswith("@"):
-- record = dict(zip(header, line.rstrip().split('\t')))
-+ record = dict(list(zip(header, line.rstrip().split('\t'))))
-
- name = record["readId"][1:]
- name, mate = name.split("/")
---- a/benchmark/scripts/evaluate_dmux.py
-+++ b/benchmark/scripts/evaluate_dmux.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- # -*- coding: utf-8 -*-
- # Copyright (c) 2014 Mikkel Schubert <MikkelSch at gmail.com>
- #
-@@ -54,7 +54,7 @@ def read_barcodes(filename):
- results = {}
- for line in open_ro(filename):
- if line.startswith("@"):
-- record = dict(zip(header, line.rstrip().split('\t')))
-+ record = dict(list(zip(header, line.rstrip().split('\t'))))
-
- name = record["readId"].split("/")[0]
- results[name] = "_".join((record["barcode_1"], record["barcode_2"]))
-@@ -90,7 +90,7 @@ def main(argv):
- if expectations[name] == barcode:
- correct += 1
- else:
-- print expectations[name], barcode
-+ print(expectations[name], barcode)
- total += 1
-
- handle.readline()
-@@ -98,7 +98,7 @@ def main(argv):
- handle.readline()
- header = handle.readline()
-
-- print total, correct
-+ print(total, correct)
-
- return 0
-
---- a/benchmark/scripts/evaluate_id.py
-+++ b/benchmark/scripts/evaluate_id.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- # -*- coding: utf-8 -*-
- # Copyright (c) 2014 Mikkel Schubert <MikkelSch at gmail.com>
- #
-@@ -56,7 +56,7 @@ class evalulate_minion(object):
- def __call__(self, readlen, insert_mean, replicate, fpath):
- prefix = os.path.join(fpath, "mate")
-
-- for method, result in self._parse_report_minion(prefix).items():
-+ for method, result in list(self._parse_report_minion(prefix).items()):
- self._results[(readlen, insert_mean, method)][replicate] = result
-
- def finalize(self):
-@@ -88,7 +88,7 @@ class evalulate_minion(object):
- results.append(result)
- result = {}
- else:
-- key, value = map(str.strip, line.split("=", 1))
-+ key, value = list(map(str.strip, line.split("=", 1)))
- result[key] = value
-
- if result:
-@@ -132,13 +132,13 @@ class evalulate_adapterrm(object):
- def print_rows(program, results):
- rows = []
- for (readlen, insert_mean, method), replicates in sorted(results.items()):
-- mean_pcr1 = numpy.mean([repl["PCR1"] for repl in replicates.values()])
-- mean_pcr2 = numpy.mean([repl["PCR2"] for repl in replicates.values()])
-+ mean_pcr1 = numpy.mean([repl["PCR1"] for repl in list(replicates.values())])
-+ mean_pcr2 = numpy.mean([repl["PCR2"] for repl in list(replicates.values())])
-
- rows.append((method, readlen, insert_mean, mean_pcr1, mean_pcr2))
-
- for row in sorted(rows):
-- print "\t".join(map(str, row))
-+ print("\t".join(map(str, row)))
-
-
- def main(argv):
-@@ -149,14 +149,14 @@ def main(argv):
- }
-
- for run in os.listdir(args.root):
-- readlen, insert_mean, replicate = map(int, run.split("_"))
-+ readlen, insert_mean, replicate = list(map(int, run.split("_")))
-
- for program in os.listdir(os.path.join(args.root, run)):
- if program in eval_funcs:
- fpath = os.path.join(args.root, run, program)
- eval_funcs[program](readlen, insert_mean, replicate, fpath)
-
-- print "\t".join(("Method", "ReadLen", "InsertMean", "PCR1", "PCR2"))
-+ print("\t".join(("Method", "ReadLen", "InsertMean", "PCR1", "PCR2")))
- for program, func in sorted(eval_funcs.items()):
- print_rows(program, func.finalize())
-
---- a/benchmark/scripts/extend_profile.py
-+++ b/benchmark/scripts/extend_profile.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- # -*- coding: utf-8 -*-
- # Copyright (c) 2014 Mikkel Schubert <MikkelSch at gmail.com>
- #
-@@ -84,13 +84,13 @@ def main(argv):
- elif not line_s or line_s.startswith("#") or line_s == "<<END":
- if rows:
- for row in sorted(rows):
-- print "\t".join(map(str, row))
-+ print("\t".join(map(str, row)))
- rows = []
- in_table = False
- in_table_header = None
- else:
-- row = dict(zip(in_table_header,
-- map(try_cast, line_s.split('\t'))))
-+ row = dict(list(zip(in_table_header,
-+ list(map(try_cast, line_s.split('\t'))))))
- row["Cycle"] = row["Cycle"] * 2
- rows.append(tuple(row[key] for key in in_table_header))
- row["Cycle"] = row["Cycle"] - 1
-@@ -99,10 +99,10 @@ def main(argv):
- elif line.startswith("["):
- in_table = True
-
-- print line,
-+ print(line, end=' ')
-
- for row in sorted(rows):
-- print "\t".join(map(str, row))
-+ print("\t".join(map(str, row)))
-
- return 0
-
---- a/benchmark/scripts/merge_tables.py
-+++ b/benchmark/scripts/merge_tables.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- # -*- coding: utf-8 -*-
- # Copyright (c) 2014 Mikkel Schubert <MikkelSch at gmail.com>
- #
-@@ -58,18 +58,18 @@ def main(argv):
- assert False, fpath
-
- for line in handle:
-- rows.append(dict(zip(header, line.rstrip().split('\t'))))
-+ rows.append(dict(list(zip(header, line.rstrip().split('\t')))))
- rows[-1]["Nth"] = str(int(replicate)) # Strip leading zeros
- rows[-1]["ReadLen"] = readlen
-
- keys.insert(0, "Nth")
- keys.insert(0, "ReadLen")
-- print "\t".join(keys)
-+ print("\t".join(keys))
- rows = ["\t".join(row.get(key, "NA") for key in keys) for row in rows]
- rows.sort()
-
- for row in rows:
-- print row
-+ print(row)
-
- return 0
-
---- a/benchmark/scripts/shuffle_fasta.py
-+++ b/benchmark/scripts/shuffle_fasta.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- # -*- coding: utf-8 -*-
- # Copyright (c) 2014 Mikkel Schubert <MikkelSch at gmail.com>
- #
-@@ -55,15 +55,15 @@ def shuffle(rng, seq):
- def main(argv):
- args = parse_args(argv)
- if args.seed is None:
-- args.seed = random.randint(0, sys.maxint)
-+ args.seed = random.randint(0, sys.maxsize)
- rng = random.Random(args.seed)
- name, sequence = read_fasta(args.file)
-
-- print "Seed =", args.seed
-- print "Seq =", sequence
-+ print("Seed =", args.seed)
-+ print("Seq =", sequence)
-
-- for _ in xrange(args.replicates - 1):
-- print "New =", shuffle(rng, sequence)
-+ for _ in range(args.replicates - 1):
-+ print("New =", shuffle(rng, sequence))
-
- return 0
-
---- a/benchmark/scripts/tabulate.py
-+++ b/benchmark/scripts/tabulate.py
-@@ -1,4 +1,4 @@
--#!/usr/bin/python
-+#!/usr/bin/python3
- # -*- coding: utf-8 -*-
- # Copyright (c) 2014 Mikkel Schubert <MikkelSch at gmail.com>
- #
-@@ -43,7 +43,7 @@ def read_table(fpath, filter_func):
- for line in handle:
- fields = line.rstrip().split("\t")
- assert len(fields) == len(header), (header, fields)
-- row = dict(zip(header, fields))
-+ row = dict(list(zip(header, fields)))
-
- name = row["Name"]
- if name.endswith("_gz") or name.endswith("_bz2"):
-@@ -90,17 +90,17 @@ def _collapse_basic(rows):
-
- subdd[key_nth] = row
-
-- for key, values in results.iteritems():
-+ for key, values in results.items():
- assert len(values) == max_nth and max(values) == max_nth, values
-
- collapsed_rows = []
- value_keys = ("SEN", "SPC", "PPV", "NPV", "MCC", "Rate")
-- for rows in results.itervalues():
-+ for rows in results.values():
- result = {}
-
- for key in value_keys:
-- if any((key in row) for row in rows.itervalues()):
-- values = tuple(float(row[key]) for row in rows.itervalues())
-+ if any((key in row) for row in rows.values()):
-+ values = tuple(float(row[key]) for row in rows.values())
- result[key] = "%.3f" % (numpy.mean(values),)
-
- for key in keys:
-@@ -138,17 +138,17 @@ def _collapse_throughput(rows):
-
- subdd[key] = row["Rate"]
-
-- for key, values in results.iteritems():
-+ for key, values in results.items():
- assert len(values) == max_nth and max(values) == max_nth, values
-
- collapsed_rows = []
- value_keys = tuple(sorted(rate_keys))
-- for rows in results.itervalues():
-+ for rows in results.values():
- result = {}
-
- for key in value_keys:
-- if any((key in row) for row in rows.itervalues()):
-- values = tuple(float(row[key]) for row in rows.itervalues())
-+ if any((key in row) for row in rows.values()):
-+ values = tuple(float(row[key]) for row in rows.values())
- result[key] = "%.1f" % (numpy.mean(values),)
-
- for key in keys:
-@@ -193,9 +193,9 @@ def main(argv):
- for row in sorted(rows):
- output_rows.append(tuple(str(row.get(key, "NA")) for key in keys))
-
-- print "\t".join(keys)
-+ print("\t".join(keys))
- for row in sorted(output_rows):
-- print "\t".join(row)
-+ print("\t".join(row))
-
- return 0
-
=====================================
debian/patches/adapt-benchmarking.patch deleted
=====================================
@@ -1,370 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 04 Dec 2016 17:31:19 +0100
-Description: Try to get benchmarking working with sensible values
-Comment: Deactivated since benchmark script vanished
-
---- a/benchmark/benchmark.sh
-+++ b/benchmark/benchmark.sh
-@@ -34,7 +34,8 @@ NUM_REPLICATES=10
- # Read lengths to examine
- # Lengths > 100 use an interpolated profile, and should therefore not be used
- # to estimate anything other than runtime (see 'simulate_reads').
--READ_LENGTHS=(100 200)
-+# READ_LENGTHS=(100 200) # 200 is accessing specific profiles which seems not to work with pIRS 2.0 syntax
-+READ_LENGTHS=(100)
-
- # Insert sizes of reads to simulate for adapter ID
- ADAPTER_ID_INSERT_SIZES=($(seq 250 5 350))
-@@ -46,11 +47,13 @@ MAX_THREADS=4
- # Number of read (pairs) to simulate using pIRS for each replicate
- SIMULATED_NREADS=1000000
-
--REFSEQ="results/reference.fasta"
--
--SIMULATED_PREFIX="results/simulated/reads"
--SIMULATED_MIXED_PREFIX="results/simulated/mixed"
--SIMULATED_ADAPTER_ID_PREFIX="results/simulated/adapter_id"
-+results=$(mktemp -d /tmp/adapter-benchmark.XXXXXX)
-+echo "*** Results will be found in $results ***"
-+REFSEQ="$results/reference.fasta"
-+
-+SIMULATED_PREFIX="$results/simulated/reads"
-+SIMULATED_MIXED_PREFIX="$results/simulated/mixed"
-+SIMULATED_ADAPTER_ID_PREFIX="$results/simulated/adapter_id"
-
-
- ###############################################################################
-@@ -84,63 +87,79 @@ function check_for_jar()
- fi
- }
-
-+echo "*** ignore old version of AdapterRemoval-1.5.4 ***"
-+#EXEC_ADAPTERREMOVAL1x="bin/AdapterRemoval-1.5.4"
-+#check_for_executable "AdapterRemoval v1.x" "${EXEC_ADAPTERREMOVAL1x}"
-+## https://github.com/slindgreen/AdapterRemoval/raw/master/AdapterRemoval-1.5.4.tar.gz
-
--EXEC_ADAPTERREMOVAL1x="bin/AdapterRemoval-1.5.4"
--check_for_executable "AdapterRemoval v1.x" "${EXEC_ADAPTERREMOVAL1x}"
--# https://github.com/slindgreen/AdapterRemoval/raw/master/AdapterRemoval-1.5.4.tar.gz
--
--EXEC_ADAPTERREMOVAL2x="bin/AdapterRemoval-2.1.3"
-+EXEC_ADAPTERREMOVAL2x="/usr/bin/AdapterRemoval"
- check_for_executable "AdapterRemoval v2.x" "${EXEC_ADAPTERREMOVAL2x}"
- # https://github.com/MikkelSchubert/adapterremoval
-
--EXEC_LEEHOM="bin/leeHom_patched"
--check_for_executable "leeHom" "${EXEC_LEEHOM}"
-+echo "*** not packaged: https://github.com/grenaud/leeHom ***"
-+#EXEC_LEEHOM="bin/leeHom_patched"
-+#check_for_executable "leeHom" "${EXEC_LEEHOM}"
- # https://github.com/grenaud/leeHom
- # -- Apply patches/leeHom.patch
-
--EXEC_SKEWER="bin/skewer"
--check_for_executable "Skewer" "${EXEC_SKEWER}"
-+echo "*** not packaged: https://github.com/relipmoc/skewer ***"
-+#EXEC_SKEWER="bin/skewer"
-+#check_for_executable "Skewer" "${EXEC_SKEWER}"
- # https://github.com/relipmoc/skewer
-
--EXEC_ALIENTRIMMER="bin/AlienTrimmer"
--check_for_executable "AlienTrimmer" "${EXEC_ALIENTRIMMER}"
-+echo "*** not packaged: ftp://ftp.pasteur.fr/pub/GenSoft/projects/AlienTrimmer/ ***"
-+#EXEC_ALIENTRIMMER="bin/AlienTrimmer"
-+#check_for_executable "AlienTrimmer" "${EXEC_ALIENTRIMMER}"
- # ftp://ftp.pasteur.fr/pub/GenSoft/projects/AlienTrimmer/
-
--EXEC_SCYTHE="bin/scythe"
-+EXEC_SCYTHE="/usr/bin/scythe"
- check_for_executable "Scythe" "${EXEC_SCYTHE}"
- # https://github.com/vsbuffalo/scythe
-
--EXEC_CUTADAPT="bin/cutadapt"
-+EXEC_CUTADAPT="/usr/bin/cutadapt"
- check_for_executable "Cutadapt" "${EXEC_CUTADAPT}"
- # https://code.google.com/p/cutadapt/
-
--EXEC_FLEXBAR="bin/flexbar"
-+EXEC_FLEXBAR="/usr/bin/flexbar"
- check_for_executable "Flexbar" "${EXEC_FLEXBAR}"
- # http://sourceforge.net/projects/flexbar/
-
--EXEC_PIRS="bin/pirs_patched"
-+EXEC_PIRS="/usr/bin/pirs"
-+if [ ! -x $EXEC_PIRS ] ; then
-+cat <<EOT
-+You need to install pIRS as /usr/bin/pirs or patch this script $0.
-+The easiest way to do so would be to create the Debian package from
-+ https://anonscm.debian.org/git/debian-med/pirs.git
-+Since it has non-distributable files there can not be an official
-+package currently.
-+EOT
-+ exit 1
-+fi
- check_for_executable "pIRS (with adapters)" "${EXEC_PIRS}"
- # ftp://ftp.genomics.org.cn/pub/pIRS/
- # -- Apply patches/pirs.patch
-
--JAR_TRIMMOMATIC="bin/trimmomatic-0.33.jar"
-+JAR_TRIMMOMATIC="/usr/share/java/trimmomatic.jar"
- check_for_jar "Trimmomatic" ${JAR_TRIMMOMATIC}
- # http://www.usadellab.org/cms/?page=trimmomatic
-
--EXEC_PEAT="./bin/PEAT"
--check_for_executable "PEAT" ${EXEC_PEAT}
-+echo "*** not packaged: https://github.com/jhhung/PEAT ***"
-+#EXEC_PEAT="./bin/PEAT"
-+#check_for_executable "PEAT" ${EXEC_PEAT}
- # https://github.com/jhhung/PEAT
-
--EXEC_PEAR="bin/pear_patched"
--check_for_executable "PEAR" ${EXEC_PEAR}
-+echo "*** not packaged: http://sco.h-its.org/exelixis/web/software/pear/ ***"
-+#EXEC_PEAR="bin/pear_patched"
-+#check_for_executable "PEAR" ${EXEC_PEAR}
- # http://sco.h-its.org/exelixis/web/software/pear/
- # -- Apply patches/pear.patch
-
--EXEC_MINION="bin/minion"
--check_for_executable "minion (kraken)" ${EXEC_MINION}
-+echo "*** not packaged: http://www.ebi.ac.uk/research/enright/software/kraken ***"
-+#EXEC_MINION="bin/minion"
-+#check_for_executable "minion (kraken)" ${EXEC_MINION}
- # http://www.ebi.ac.uk/research/enright/software/kraken
-
--EXEC_FASTQ_MCF="bin/fastq-mcf"
-+EXEC_FASTQ_MCF="/usr/bin/fastq-mcf"
- check_for_executable "fastq-mcf" ${EXEC_FASTQ_MCF}
- # https://code.google.com/p/ea-utils/
-
-@@ -149,7 +168,7 @@ EXEC_TIME=/usr/bin/time
- check_for_executable "GNU time" ${EXEC_TIME}
- # Needed for time / RAM usage
-
--EXEC_JAVA="bin/java"
-+EXEC_JAVA="/usr/bin/java"
- check_for_executable "Java JRE" ${EXEC_JAVA}
- # Needed for Trimmomatic
-
-@@ -240,14 +259,16 @@ function fetch_reference()
- echo "------------------------------------------------------------" > /dev/stderr
- echo "Fetching reference sequence ..." > /dev/stderr
-
-- if [ -e "results/reference.fasta" ];
-+ if [ -e "$results/reference.fasta" ];
- then
- echo "Reference sequence found; skipping ..." > /dev/stderr
- echo "" > /dev/stderr
- else
- echo "" > /dev/stderr
-- wget -O results/reference.fasta.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz
-- gunzip results/reference.fasta.gz
-+# wget -O $results/reference.fasta.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz
-+# gunzip $results/reference.fasta.gz
-+echo "FIXME!!!!!"
-+cp -a /tmp/adapter-benchmark/reference.fasta $results
- fi
-
-
-@@ -268,7 +289,8 @@ function simulate_reads()
- if [ "${readlen}" -gt 100 ];
- then
- # Use fake profiles, built using scripts/extend_profile.py
-- PROFILE_CLI="-b profiles/phixv2.InDel.matrix -s profiles/humNew.PE100.matrix.gz"
-+ # PROFILE_CLI="-b profiles/phixv2.InDel.matrix -s profiles/humNew.PE100.matrix.gz"
-+ PROFILE_CLI="--indel-profile=profiles/phixv2.InDel.matrix --base-calling-profile=profiles/humNew.PE100.matrix.gz"
- else
- PROFILE_CLI=
- fi
-@@ -285,15 +307,19 @@ function simulate_reads()
- rm -rf "${DST:?}/"
- mkdir -p "${DST}/"
-
-- # -c 0 = uncompressed output
-- if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" -i "${REFSEQ}" -c 0 -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
-+ # -c text = uncompressed output
-+ set -x
-+ if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c text -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
- > "${DST}/reads.stdout" 2> "${DST}/reads.stderr";
- then
- echo "Error simulated reads ..." > /dev/stderr
- exit 1
- fi
-+ set +x
-
-- gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz"
-+ if [ -e "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz" ] ; then
-+ gunzip "${DST}/reads_${readlen}_${INSERT_MEAN}.read.info.gz"
-+ fi
- ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_1.fq" "${DST}_1.fq"
- ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}_2.fq" "${DST}_2.fq"
- ln -sf "$(basename "${DST}")/reads_${readlen}_${INSERT_MEAN}.read.info" "${DST}.read.info"
-@@ -813,14 +839,16 @@ function benchmark_se()
- SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq"
- SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq"
- SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info"
-- RESULTS="results/se/${readlen}_${run_n}"
-+ RESULTS="$results/se/${readlen}_${run_n}"
-
- # -mm 3 corresponds to AR 2.x defaults
-- echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL1x} 1 \
-- "${RESULTS}/adapterremoval1x_mm3" \
-- "${SIMULATED_INFO}" \
-- --file1 "${SIMULATED_MATE1}" \
-- --mm 3
-+ if [ -z ${EXEC_ADAPTERREMOVAL1x+x} ] ; then
-+ echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL1x} 1 \
-+ "${RESULTS}/adapterremoval1x_mm3" \
-+ "${SIMULATED_INFO}" \
-+ --file1 "${SIMULATED_MATE1}" \
-+ --mm 3
-+ fi
-
- # -mm 3 --minadapteroverlap 3 (test)
- echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} 1 \
-@@ -901,7 +929,7 @@ function benchmark_se()
- done
- done
-
-- ${SCRIPT_MERGE} results/se > results/se.table
-+ ${SCRIPT_MERGE} $results/se > $results/se.table
- }
-
-
-@@ -921,17 +949,19 @@ function benchmark_pe()
- SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq"
- SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq"
- SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info"
-- RESULTS="results/pe/${readlen}_${run_n}"
-+ RESULTS="$results/pe/${readlen}_${run_n}"
-
- DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-
- # -mm 3 corresponds to AR 2.x defaults
-- echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL1x} 1 \
-- "${RESULTS}/adapterremoval1x_mm3" \
-- "${SIMULATED_INFO}" \
-- --file1 "${SIMULATED_MATE1}" \
-- --file2 "${SIMULATED_MATE2}" \
-- --mm 3
-+ if [ -z ${EXEC_ADAPTERREMOVAL1x+x} ] ; then
-+ echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL1x} 1 \
-+ "${RESULTS}/adapterremoval1x_mm3" \
-+ "${SIMULATED_INFO}" \
-+ --file1 "${SIMULATED_MATE1}" \
-+ --file2 "${SIMULATED_MATE2}" \
-+ --mm 3
-+ fi
-
- for nthreads in $(seq 1 ${MAX_THREADS});
- do
-@@ -997,7 +1027,7 @@ function benchmark_pe()
- done
- done
-
-- ${SCRIPT_MERGE} results/pe > results/pe.table
-+ ${SCRIPT_MERGE} $results/pe > $results/pe.table
- }
-
-
-@@ -1017,17 +1047,19 @@ function benchmark_collapse()
- SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq"
- SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq"
- SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info"
-- RESULTS="results/collapse/${readlen}_${run_n}"
-+ RESULTS="$results/collapse/${readlen}_${run_n}"
-
- DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-
- # -mm 3 corresponds to AR 2.x defaults
-- echo run_adapterremoval COLLAPSE ${EXEC_ADAPTERREMOVAL1x} 1 \
-- "${RESULTS}/adapterremoval1x_mm3" \
-- "${SIMULATED_INFO}" \
-- --file1 "${SIMULATED_MATE1}" \
-- --file2 "${SIMULATED_MATE2}" \
-- --mm 3 --collapse
-+ if [ -z ${EXEC_ADAPTERREMOVAL1x+x} ] ; then
-+ echo run_adapterremoval COLLAPSE ${EXEC_ADAPTERREMOVAL1x} 1 \
-+ "${RESULTS}/adapterremoval1x_mm3" \
-+ "${SIMULATED_INFO}" \
-+ --file1 "${SIMULATED_MATE1}" \
-+ --file2 "${SIMULATED_MATE2}" \
-+ --mm 3 --collapse
-+ fi
-
- for nthreads in $(seq 1 ${MAX_THREADS});
- do
-@@ -1063,7 +1095,7 @@ function benchmark_collapse()
- done
- done
-
-- ${SCRIPT_MERGE} results/collapse > results/collapse.table
-+ ${SCRIPT_MERGE} $results/collapse > $results/collapse.table
- }
-
-
-@@ -1084,7 +1116,7 @@ function benchmark_mixed_se
- SIMULATED_MATE1="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_1.fq"
- SIMULATED_MATE2="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_2.fq"
- SIMULATED_INFO="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}.read.info"
-- RESULTS="results/mixed_se/${readlen}_${run_n}"
-+ RESULTS="$results/mixed_se/${readlen}_${run_n}"
-
- DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
- AR_PREFIX="${RESULTS}/adapterremoval2x"
-@@ -1139,7 +1171,7 @@ function benchmark_mixed_se
- done
- done
-
-- ${SCRIPT_MERGE} results/mixed_se > results/mixed_se.table
-+ ${SCRIPT_MERGE} $results/mixed_se > $results/mixed_se.table
- }
-
-
-@@ -1159,7 +1191,7 @@ function benchmark_mixed_pe
- SIMULATED_MATE1="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_1.fq"
- SIMULATED_MATE2="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}_2.fq"
- SIMULATED_INFO="${SIMULATED_MIXED_PREFIX}_${run_n}_${readlen}.read.info"
-- RESULTS="results/mixed_pe/${readlen}_${run_n}"
-+ RESULTS="$results/mixed_pe/${readlen}_${run_n}"
-
- DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-
-@@ -1204,7 +1236,7 @@ function benchmark_mixed_pe
- done
- done
-
-- ${SCRIPT_MERGE} results/mixed_pe > results/mixed_pe.table
-+ ${SCRIPT_MERGE} $results/mixed_pe > $results/mixed_pe.table
- }
-
-
-@@ -1224,7 +1256,7 @@ function benchmark_adapter_id
- SIMULATED_MATE1="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}_1.fq"
- SIMULATED_MATE2="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}_2.fq"
- SIMULATED_INFO="${SIMULATED_ADAPTER_ID_PREFIX}_${run_n}_${readlen}_${INSERT_MEAN}.read.info"
-- RESULTS="results/adapter_id/${readlen}_${INSERT_MEAN}_${run_n}"
-+ RESULTS="$results/adapter_id/${readlen}_${INSERT_MEAN}_${run_n}"
-
- run_minion "${RESULTS}/minion" \
- "${SIMULATED_MATE1}" \
-@@ -1236,15 +1268,17 @@ function benchmark_adapter_id
- done
- done
-
-- ${SCRIPT_EVALUATE_ID} results/adapter_id > results/adapter_id.table
-+ ${SCRIPT_EVALUATE_ID} $results/adapter_id > $results/adapter_id.table
- }
-
-
-
- cd "$(dirname "$0")"
--mkdir -p results
-+pwd
-+#mkdir -p results
-
- fetch_reference
-+cp -a profiles $results
-
- echo > /dev/stderr
-
=====================================
debian/patches/delete_adapterremoval1x_completely.patch deleted
=====================================
@@ -1,85 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 04 Dec 2016 17:31:19 +0100
-Description: Remove not (yet) packaged adapters
-Comment: Deactivated since benchmark script vanished
-
---- a/benchmark/benchmark.sh
-+++ b/benchmark/benchmark.sh
-@@ -843,15 +843,6 @@ function benchmark_se()
- SIMULATED_INFO="${SIMULATED_PREFIX}_${run_n}_${readlen}.read.info"
- RESULTS="$results/se/${readlen}_${run_n}"
-
-- # -mm 3 corresponds to AR 2.x defaults
-- if [ -z ${EXEC_ADAPTERREMOVAL1x+x} ] ; then
-- echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL1x} 1 \
-- "${RESULTS}/adapterremoval1x_mm3" \
-- "${SIMULATED_INFO}" \
-- --file1 "${SIMULATED_MATE1}" \
-- --mm 3
-- fi
--
- # -mm 3 --minadapteroverlap 3 (test)
- echo run_adapterremoval SE ${EXEC_ADAPTERREMOVAL2x} 1 \
- "${RESULTS}/adapterremoval2x_min3_mm3" \
-@@ -912,16 +903,18 @@ function benchmark_se()
- -c "adapters/adapter_1.txt" \
- -q 0
-
-- echo run_leeHom SE \
-- "${RESULTS}/leeHom" \
-- "${SIMULATED_INFO}" \
-- -fq1 "${SIMULATED_MATE1}"
-+ if [ -z ${EXEC_LEEHOM+x} ]; then
-+ echo run_leeHom SE \
-+ "${RESULTS}/leeHom" \
-+ "${SIMULATED_INFO}" \
-+ -fq1 "${SIMULATED_MATE1}"
-
-- echo run_leeHom SE \
-- "${RESULTS}/leeHom_ancient" \
-- "${SIMULATED_INFO}" \
-- -fq1 "${SIMULATED_MATE1}" \
-- --ancientdna
-+ echo run_leeHom SE \
-+ "${RESULTS}/leeHom_ancient" \
-+ "${SIMULATED_INFO}" \
-+ -fq1 "${SIMULATED_MATE1}" \
-+ --ancientdna
-+ fi
-
- echo run_fastq_mcf_se "${RESULTS}/fastq_mcf" \
- "${SIMULATED_INFO}" \
-@@ -955,16 +948,6 @@ function benchmark_pe()
-
- DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-
-- # -mm 3 corresponds to AR 2.x defaults
-- if [ -z ${EXEC_ADAPTERREMOVAL1x+x} ] ; then
-- echo run_adapterremoval PE ${EXEC_ADAPTERREMOVAL1x} 1 \
-- "${RESULTS}/adapterremoval1x_mm3" \
-- "${SIMULATED_INFO}" \
-- --file1 "${SIMULATED_MATE1}" \
-- --file2 "${SIMULATED_MATE2}" \
-- --mm 3
-- fi
--
- for nthreads in $(seq 1 ${MAX_THREADS});
- do
- AR_PREFIX="${RESULTS}/adapterremoval2x"
-@@ -1053,16 +1036,6 @@ function benchmark_collapse()
-
- DEFAULT_ARGS=("${SIMULATED_INFO}" "${SIMULATED_MATE1}" "${SIMULATED_MATE2}")
-
-- # -mm 3 corresponds to AR 2.x defaults
-- if [ -z ${EXEC_ADAPTERREMOVAL1x+x} ] ; then
-- echo run_adapterremoval COLLAPSE ${EXEC_ADAPTERREMOVAL1x} 1 \
-- "${RESULTS}/adapterremoval1x_mm3" \
-- "${SIMULATED_INFO}" \
-- --file1 "${SIMULATED_MATE1}" \
-- --file2 "${SIMULATED_MATE2}" \
-- --mm 3 --collapse
-- fi
--
- for nthreads in $(seq 1 ${MAX_THREADS});
- do
- AR_PREFIX="${RESULTS}/adapterremoval2x"
=====================================
debian/patches/reduce_benchmark_length.patch deleted
=====================================
@@ -1,29 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 04 Dec 2016 17:31:19 +0100
-Description: There is no point in uselessly consuming computing
- power for a simple test - so drastically reduce length of data sets
-Comment: Deactivated since benchmark script vanished
-
---- a/benchmark/benchmark.sh
-+++ b/benchmark/benchmark.sh
-@@ -45,7 +45,7 @@ ADAPTER_ID_INSERT_SIZES=($(seq 250 5 350
- MAX_THREADS=4
-
- # Number of read (pairs) to simulate using pIRS for each replicate
--SIMULATED_NREADS=1000000
-+SIMULATED_NREADS=100
-
- results=$(mktemp -d /tmp/adapter-benchmark.XXXXXX)
- echo "*** Results will be found in $results ***"
-@@ -267,8 +267,10 @@ function fetch_reference()
- echo "" > /dev/stderr
- # wget -O $results/reference.fasta.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz
- # gunzip $results/reference.fasta.gz
-+ cp -a /usr/share/doc/pirs/examples/pirs/ref_seq.fa.gz $results/reference.fasta.gz
-+ gunzip $results/reference.fasta.gz
- echo "FIXME!!!!!"
--cp -a /tmp/adapter-benchmark/reference.fasta $results
-+#cp -a /tmp/adapter-benchmark/reference.fasta $results
- fi
-
-
=====================================
debian/patches/series deleted
=====================================
@@ -1,5 +0,0 @@
-#adapt-benchmarking.patch
-#reduce_benchmark_length.patch
-#delete_adapterremoval1x_completely.patch
-#2to3.patch
-update-catch2.patch
=====================================
debian/patches/update-catch2.patch deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
docs/conf.py
=====================================
@@ -54,9 +54,9 @@ author = u'Mikkel Schubert; Stinus Lindgreen'
# built documents.
#
# The short X.Y version.
-version = u'2.3.2'
+version = u'2.3.3'
# The full version, including alpha/beta/rc tags.
-release = u'2.3.2'
+release = u'2.3.3'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
=====================================
src/main.hpp
=====================================
@@ -31,7 +31,7 @@ namespace ar
{
const std::string NAME = "AdapterRemoval";
-const std::string VERSION = "ver. 2.3.2";
+const std::string VERSION = "ver. 2.3.3";
const std::string HELPTEXT = \
"This program searches for and removes remnant adapter sequences from\n"
"your read data. The program can analyze both single end and paired end\n"
=====================================
tests/unit/catch.hpp
=====================================
The diff for this file was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/adapterremoval/-/compare/1a9fe64aba6141be242baa184454b4d29bf35cf1...bc20bcb7fa78f76a5545c6ac2b7d2c1f3931b73d
--
View it on GitLab: https://salsa.debian.org/med-team/adapterremoval/-/compare/1a9fe64aba6141be242baa184454b4d29bf35cf1...bc20bcb7fa78f76a5545c6ac2b7d2c1f3931b73d
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