[med-svn] [Git][med-team/fastp][master] 4 commits: Add d/clean to clean redundant files
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Sep 5 22:17:16 BST 2021
Nilesh Patra pushed to branch master at Debian Med / fastp
Commits:
b64c75f4 by Nilesh Patra at 2021-09-06T00:37:48+05:30
Add d/clean to clean redundant files
- - - - -
fc218855 by Nilesh Patra at 2021-09-05T19:14:07+00:00
Add manpage, remove generation of manpage at build time
- - - - -
6d0255e3 by Nilesh Patra at 2021-09-05T21:04:30+00:00
d/p/fix-i386.patch: Fix autopkgtests on armhf and i386
- - - - -
9d7f08f4 by Nilesh Patra at 2021-09-06T02:42:44+05:30
Upload to unstable
- - - - -
9 changed files:
- debian/changelog
- + debian/clean
- debian/control
- + debian/createmanpages
- + debian/fastp.1
- + debian/manpages
- + debian/patches/fix-i386.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+fastp (0.22.0+dfsg-2) unstable; urgency=medium
+
+ * Team Upload.
+ * Add d/clean to clean redundant files and dirs
+ * Add maintainer manpage, remove generation of manpage at build time
+ + Helps package cross build
+ * d/p/fix-i386.patch: Fix autopkgtests on armhf and i386
+
+ -- Nilesh Patra <nilesh at debian.org> Mon, 06 Sep 2021 02:38:45 +0530
+
fastp (0.22.0+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/clean
=====================================
@@ -0,0 +1,2 @@
+obj/
+fastp
=====================================
debian/control
=====================================
@@ -4,7 +4,6 @@ Uploaders: Dylan Aïssi <daissi at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
- help2man,
zlib1g-dev
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/fastp
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/fastp.1
=====================================
@@ -0,0 +1,267 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH FASTP "1" "September 2021" "fastp 0.22.0" "User Commands"
+.SH NAME
+fastp \- Ultra-fast all-in-one FASTQ preprocessor
+.SH DESCRIPTION
+fastp: an ultra\-fast all\-in\-one FASTQ preprocessor
+version 0.22.0
+usage: fastp [options] ...
+options:
+.TP
+\fB\-i\fR, \fB\-\-in1\fR
+read1 input file name (string [=])
+.TP
+\fB\-o\fR, \fB\-\-out1\fR
+read1 output file name (string [=])
+.TP
+\fB\-I\fR, \fB\-\-in2\fR
+read2 input file name (string [=])
+.TP
+\fB\-O\fR, \fB\-\-out2\fR
+read2 output file name (string [=])
+.TP
+\fB\-D\fR, \fB\-\-dedup\fR
+enable deduplication to drop the duplicated reads/pairs
+.TP
+\fB\-\-unpaired1\fR
+for PE input, if read1 passed QC but read2 not, it will be written to unpaired1. Default is to discard it. (string [=])
+.TP
+\fB\-\-unpaired2\fR
+for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If \fB\-\-unpaired2\fR is same as \fB\-\-unpaired1\fR (default mode), both unpaired reads will be written to this same file. (string [=])
+.TP
+\fB\-\-overlapped_out\fR
+for each read pair, output the overlapped region if it has no any mismatched base. (string [=])
+.TP
+\fB\-\-failed_out\fR
+specify the file to store reads that cannot pass the filters. (string [=])
+.TP
+\fB\-m\fR, \fB\-\-merge\fR
+for paired\-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by \fB\-\-merged_out\fR, the unmerged reads will be written to the files specified by \fB\-\-out1\fR and \fB\-\-out2\fR. The merging mode is disabled by default.
+.TP
+\fB\-\-merged_out\fR
+in the merging mode, specify the file name to store merged output, or specify \fB\-\-stdout\fR to stream the merged output (string [=])
+.TP
+\fB\-\-include_unmerged\fR
+in the merging mode, write the unmerged or unpaired reads to the file specified by \fB\-\-merge\fR. Disabled by default.
+.TP
+\fB\-6\fR, \fB\-\-phred64\fR
+indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
+.TP
+\fB\-z\fR, \fB\-\-compression\fR
+compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4. (int [=4])
+.TP
+\fB\-\-stdin\fR
+input from STDIN. If the STDIN is interleaved paired\-end FASTQ, please also add \fB\-\-interleaved_in\fR.
+.TP
+\fB\-\-stdout\fR
+stream passing\-filters reads to STDOUT. This option will result in interleaved FASTQ output for paired\-end output. Disabled by default.
+.TP
+\fB\-\-interleaved_in\fR
+indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by default.
+.TP
+\fB\-\-reads_to_process\fR
+specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])
+.TP
+\fB\-\-dont_overwrite\fR
+don't overwrite existing files. Overwritting is allowed by default.
+.TP
+\fB\-\-dont_eval_duplication\fR
+don't evaluate duplication rate to save time and use less memory.
+.TP
+\fB\-\-fix_mgi_id\fR
+the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.
+.TP
+\fB\-V\fR, \fB\-\-verbose\fR
+output verbose log information (i.e. when every 1M reads are processed).
+.TP
+\fB\-A\fR, \fB\-\-disable_adapter_trimming\fR
+adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
+.TP
+\fB\-a\fR, \fB\-\-adapter_sequence\fR
+the adapter for read1. For SE data, if not specified, the adapter will be auto\-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto])
+.TP
+\fB\-\-adapter_sequence_r2\fR
+the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as <adapter_sequence> (string [=auto])
+.TP
+\fB\-\-adapter_fasta\fR
+specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file (string [=])
+.TP
+\fB\-\-detect_adapter_for_pe\fR
+by default, the auto\-detection for adapter is for SE data input only, turn on this option to enable it for PE data.
+.TP
+\fB\-f\fR, \fB\-\-trim_front1\fR
+trimming how many bases in front for read1, default is 0 (int [=0])
+.TP
+\fB\-t\fR, \fB\-\-trim_tail1\fR
+trimming how many bases in tail for read1, default is 0 (int [=0])
+.TP
+\fB\-b\fR, \fB\-\-max_len1\fR
+if read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1. Default 0 means no limitation (int [=0])
+.TP
+\fB\-F\fR, \fB\-\-trim_front2\fR
+trimming how many bases in front for read2. If it's not specified, it will follow read1's settings (int [=0])
+.TP
+\fB\-T\fR, \fB\-\-trim_tail2\fR
+trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0])
+.TP
+\fB\-B\fR, \fB\-\-max_len2\fR
+if read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2. Default 0 means no limitation. If it's not specified, it will follow read1's settings (int [=0])
+.TP
+\fB\-g\fR, \fB\-\-trim_poly_g\fR
+force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
+.TP
+\fB\-\-poly_g_min_len\fR
+the minimum length to detect polyG in the read tail. 10 by default. (int [=10])
+.TP
+\fB\-G\fR, \fB\-\-disable_trim_poly_g\fR
+disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
+.TP
+\fB\-x\fR, \fB\-\-trim_poly_x\fR
+enable polyX trimming in 3' ends.
+.TP
+\fB\-\-poly_x_min_len\fR
+the minimum length to detect polyX in the read tail. 10 by default. (int [=10])
+.TP
+\fB\-5\fR, \fB\-\-cut_front\fR
+move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise.
+.TP
+\fB\-3\fR, \fB\-\-cut_tail\fR
+move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise.
+.TP
+\fB\-r\fR, \fB\-\-cut_right\fR
+move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop.
+.TP
+\fB\-W\fR, \fB\-\-cut_window_size\fR
+the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4 (int [=4])
+.TP
+\fB\-M\fR, \fB\-\-cut_mean_quality\fR
+the mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20) (int [=20])
+.TP
+\fB\-\-cut_front_window_size\fR
+the window size option of cut_front, default to cut_window_size if not specified (int [=4])
+.TP
+\fB\-\-cut_front_mean_quality\fR
+the mean quality requirement option for cut_front, default to cut_mean_quality if not specified (int [=20])
+.TP
+\fB\-\-cut_tail_window_size\fR
+the window size option of cut_tail, default to cut_window_size if not specified (int [=4])
+.TP
+\fB\-\-cut_tail_mean_quality\fR
+the mean quality requirement option for cut_tail, default to cut_mean_quality if not specified (int [=20])
+.TP
+\fB\-\-cut_right_window_size\fR
+the window size option of cut_right, default to cut_window_size if not specified (int [=4])
+.TP
+\fB\-\-cut_right_mean_quality\fR
+the mean quality requirement option for cut_right, default to cut_mean_quality if not specified (int [=20])
+.TP
+\fB\-Q\fR, \fB\-\-disable_quality_filtering\fR
+quality filtering is enabled by default. If this option is specified, quality filtering is disabled
+.TP
+\fB\-q\fR, \fB\-\-qualified_quality_phred\fR
+the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
+.TP
+\fB\-u\fR, \fB\-\-unqualified_percent_limit\fR
+how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
+.TP
+\fB\-n\fR, \fB\-\-n_base_limit\fR
+if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
+.TP
+\fB\-e\fR, \fB\-\-average_qual\fR
+if one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means no requirement (int [=0])
+.TP
+\fB\-L\fR, \fB\-\-disable_length_filtering\fR
+length filtering is enabled by default. If this option is specified, length filtering is disabled
+.TP
+\fB\-l\fR, \fB\-\-length_required\fR
+reads shorter than length_required will be discarded, default is 15. (int [=15])
+.TP
+\fB\-\-length_limit\fR
+reads longer than length_limit will be discarded, default 0 means no limitation. (int [=0])
+.TP
+\fB\-y\fR, \fB\-\-low_complexity_filter\fR
+enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).
+.TP
+\fB\-Y\fR, \fB\-\-complexity_threshold\fR
+the threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required. (int [=30])
+.TP
+\fB\-\-filter_by_index1\fR
+specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line (string [=])
+.TP
+\fB\-\-filter_by_index2\fR
+specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line (string [=])
+.TP
+\fB\-\-filter_by_index_threshold\fR
+the allowed difference of index barcode for index filtering, default 0 means completely identical. (int [=0])
+.TP
+\fB\-c\fR, \fB\-\-correction\fR
+enable base correction in overlapped regions (only for PE data), default is disabled
+.TP
+\fB\-\-overlap_len_require\fR
+the minimum length to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 30 by default. (int [=30])
+.TP
+\fB\-\-overlap_diff_limit\fR
+the maximum number of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 5 by default. (int [=5])
+.TP
+\fB\-\-overlap_diff_percent_limit\fR
+the maximum percentage of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%. (int [=20])
+.TP
+\fB\-U\fR, \fB\-\-umi\fR
+enable unique molecular identifier (UMI) preprocessing
+.TP
+\fB\-\-umi_loc\fR
+specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=])
+.TP
+\fB\-\-umi_len\fR
+if the UMI is in read1/read2, its length should be provided (int [=0])
+.TP
+\fB\-\-umi_prefix\fR
+if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=])
+.TP
+\fB\-\-umi_skip\fR
+if the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0 (int [=0])
+.TP
+\fB\-p\fR, \fB\-\-overrepresentation_analysis\fR
+enable overrepresented sequence analysis.
+.TP
+\fB\-P\fR, \fB\-\-overrepresentation_sampling\fR
+one in (\fB\-\-overrepresentation_sampling\fR) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20])
+.TP
+\fB\-j\fR, \fB\-\-json\fR
+the json format report file name (string [=fastp.json])
+.TP
+\fB\-h\fR, \fB\-\-html\fR
+the html format report file name (string [=fastp.html])
+.TP
+\fB\-R\fR, \fB\-\-report_title\fR
+should be quoted with ' or ", default is "fastp report" (string [=fastp report])
+.TP
+\fB\-w\fR, \fB\-\-thread\fR
+worker thread number, default is 2 (int [=2])
+.TP
+\fB\-s\fR, \fB\-\-split\fR
+split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
+.TP
+\fB\-S\fR, \fB\-\-split_by_lines\fR
+split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0])
+.TP
+\fB\-d\fR, \fB\-\-split_prefix_digits\fR
+the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding (int [=4])
+.TP
+\fB\-\-cut_by_quality5\fR
+DEPRECATED, use \fB\-\-cut_front\fR instead.
+.TP
+\fB\-\-cut_by_quality3\fR
+DEPRECATED, use \fB\-\-cut_tail\fR instead.
+.TP
+\fB\-\-cut_by_quality_aggressive\fR
+DEPRECATED, use \fB\-\-cut_right\fR instead.
+.TP
+\fB\-\-discard_unmerged\fR
+DEPRECATED, no effect now, see the introduction for merging.
+.TP
+\-?, \fB\-\-help\fR
+print this message
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/patches/fix-i386.patch
=====================================
@@ -0,0 +1,23 @@
+Description: Fix defines to correct values
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-09-05
+--- a/src/common.h
++++ b/src/common.h
+@@ -5,12 +5,12 @@
+
+ #define _DEBUG false
+
+-#ifndef _WIN32
+- typedef long int64;
+- typedef unsigned long uint64;
++#if defined(__arm__) || defined(__i386__)
++ typedef long long int64;
++ typedef unsigned long long uint64;
+ #else
+- typedef long long int64;
+- typedef unsigned long long uint64;
++ typedef long int64;
++ typedef unsigned long uint64;
+ #endif
+
+ typedef int int32;
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
makefile.patch
+fix-i386.patch
=====================================
debian/rules
=====================================
@@ -10,9 +10,5 @@ override_dh_auto_clean:
override_dh_auto_build:
dh_auto_build
- help2man --no-discard-stderr --name="ultra-fast all-in-one FASTQ preprocessor" ./fastp > fastp.1
override_dh_auto_install:
-
-override_dh_installman:
- dh_installman fastp.1
View it on GitLab: https://salsa.debian.org/med-team/fastp/-/compare/424e5ca91edb3ec999722793de1ad6b5baeec727...9d7f08f4b7c3b1c64c1d6ecd7cb437ecd5e178c6
--
View it on GitLab: https://salsa.debian.org/med-team/fastp/-/compare/424e5ca91edb3ec999722793de1ad6b5baeec727...9d7f08f4b7c3b1c64c1d6ecd7cb437ecd5e178c6
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