[med-svn] [Git][med-team/flash][master] 3 commits: Install changelog

Tue May 26 12:31:00 BST 2020


Andreas Tille pushed to branch master at Debian Med / flash


Commits:
1887d572 by Andreas Tille at 2020-05-26T12:34:18+02:00
Install changelog

- - - - -
82c30b63 by Andreas Tille at 2020-05-26T12:50:00+02:00
Add manpage

- - - - -
36402d4b by Andreas Tille at 2020-05-26T13:30:43+02:00
Add ITP bug number

- - - - -


5 changed files:

- debian/changelog
- + debian/createmanpages
- + debian/flash.1
- + debian/manpages
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-flash (1.2.11-1) UNRELEASED; urgency=medium
+flash (1.2.11-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #961587)
 
- -- Andreas Tille <tille at debian.org>  Tue, 26 May 2020 11:53:59 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 26 May 2020 13:30:31 +0200


=====================================
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=" --help" \
+         --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/flash.1
=====================================
@@ -0,0 +1,282 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
+.TH FLASH "1" "May 2020" "flash 1.2.11" "User Commands"
+.SH NAME
+flash \- Fast Length Adjustment of SHort reads
+.SH SYNOPSIS
+.B flash
+[\fI\,OPTIONS\/\fR] \fI\,MATES_1.FASTQ MATES_2.FASTQ\/\fR
+.PP
+.B flash
+[\fI\,OPTIONS\fR] \fB\-\-interleaved\-input\fR (MATES.FASTQ | \-)
+.PP
+.B flash
+[\FIOPTIONS\fR] \fB\-\-tab\-delimited\-input\fR (MATES.TAB | \-)
+.SH DESCRIPTION
+FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool
+to merge paired\-end reads that were generated from DNA fragments whose
+lengths are shorter than twice the length of reads.  Merged read pairs result
+in unpaired longer reads, which are generally more desired in genome
+assembly and genome analysis processes.
+.PP
+Briefly, the FLASH algorithm considers all possible overlaps at or above a
+minimum length between the reads in a pair and chooses the overlap that
+results in the lowest mismatch density (proportion of mismatched bases in
+the overlapped region).  Ties between multiple overlaps are broken by
+considering quality scores at mismatch sites.  When building the merged
+sequence, FLASH computes a consensus sequence in the overlapped region.
+More details can be found in the original publication
+(http://bioinformatics.oxfordjournals.org/content/27/21/2957.full).
+.SS "Limitations of FLASH include:"
+.IP
+\- FLASH cannot merge paired\-end reads that do not overlap.
+.IP
+\- FLASH is not designed for data that has a significant amount of indel
+errors (such as Sanger sequencing data).
+It is best suited for Illumina data.
+.PP
+.SH MANDATORY INPUT
+The most common input to FLASH is two FASTQ files containing read 1 and read 2
+of each mate pair, respectively, in the same order.
+.PP
+Alternatively, you may provide one FASTQ file, which may be standard input,
+containing paired\-end reads in either interleaved FASTQ (see the
+\fB\-\-interleaved\-input\fR option) or tab\-delimited (see the \fB\-\-tab\-delimited\-input\fR
+option) format.  In all cases, gzip compressed input is autodetected.  Also,
+in all cases, the PHRED offset is, by default, assumed to be 33; use the
+\fB\-\-phred\-offset\fR option to change it.
+.SH OUTPUT
+The default output of FLASH consists of the following files:
+.TP
+\- out.extendedFrags.fastq
+The merged reads.
+.TP
+\- out.notCombined_1.fastq
+Read 1 of mate pairs that were not merged.
+.TP
+\- out.notCombined_2.fastq
+Read 2 of mate pairs that were not merged.
+.TP
+\- out.hist
+Numeric histogram of merged read lengths.
+.TP
+\- out.histogram
+Visual histogram of merged read lengths.
+.PP
+FLASH also logs informational messages to standard output.  These can also be
+redirected to a file, as in the following example:
+.IP
+\f(CW$ flash reads_1.fq reads_2.fq 2>&1 | tee flash.log\fR
+.PP
+In addition, FLASH supports several features affecting the output:
+.IP
+\- Writing the merged reads directly to standard output (\fB\-\-to\-stdout\fR)
+.IP
+\- Writing gzip compressed output files (\fB\-z\fR) or using an external
+   compression program (\fB\-\-compress\-prog\fR)
+.IP
+\- Writing the uncombined read pairs in interleaved FASTQ format
+.IP
+(\fB\-\-interleaved\-output\fR)
+.IP
+\- Writing all output reads to a single file in tab\-delimited format
+.IP
+(\fB\-\-tab\-delimited\-output\fR)
+.SH OPTIONS
+.TP
+\fB\-m\fR, \fB\-\-min\-overlap\fR=\fI\,NUM\/\fR
+The minimum required overlap length between two
+reads to provide a confident overlap.  Default:
+10bp.
+.TP
+\fB\-M\fR, \fB\-\-max\-overlap\fR=\fI\,NUM\/\fR
+Maximum overlap length expected in approximately
+90% of read pairs.  It is by default set to 65bp,
+which works well for 100bp reads generated from a
+180bp library, assuming a normal distribution of
+fragment lengths.  Overlaps longer than the maximum
+overlap parameter are still considered as good
+overlaps, but the mismatch density (explained below)
+is calculated over the first max_overlap bases in
+the overlapped region rather than the entire
+overlap.  Default: 65bp, or calculated from the
+specified read length, fragment length, and fragment
+length standard deviation.
+.TP
+\fB\-x\fR, \fB\-\-max\-mismatch\-density\fR=\fI\,NUM\/\fR
+Maximum allowed ratio between the number of
+mismatched base pairs and the overlap length.
+Two reads will not be combined with a given overlap
+if that overlap results in a mismatched base density
+higher than this value.  Note: Any occurence of an
+\&'N' in either read is ignored and not counted
+towards the mismatches or overlap length.  Our
+experimental results suggest that higher values of
+the maximum mismatch density yield larger
+numbers of correctly merged read pairs but at
+the expense of higher numbers of incorrectly
+merged read pairs.  Default: 0.25.
+.TP
+\fB\-O\fR, \fB\-\-allow\-outies\fR
+Also try combining read pairs in the "outie"
+orientation, e.g.
+.TP
+Read 1: <\-\-\-\-\-\-\-\-\-\-\-
+Read 2:       \fB\-\-\-\-\-\-\-\-\-\-\-\-\fR>
+.IP
+as opposed to only the "innie" orientation, e.g.
+.TP
+Read 1:
+<\-\-\-\-\-\-\-\-\-\-\-\-
+.IP
+Read 2: \fB\-\-\-\-\-\-\-\-\-\-\-\fR>
+.TP
+FLASH uses the same parameters when trying each
+orientation.  If a read pair can be combined in
+both "innie" and "outie" orientations, the
+better\-fitting one will be chosen using the same
+scoring algorithm that FLASH normally uses.
+.TP
+This option also causes extra .innie and .outie
+histogram files to be produced.
+.TP
+\fB\-p\fR, \fB\-\-phred\-offset\fR=\fI\,OFFSET\/\fR
+The smallest ASCII value of the characters used to
+represent quality values of bases in FASTQ files.
+It should be set to either 33, which corresponds
+to the later Illumina platforms and Sanger
+platforms, or 64, which corresponds to the
+earlier Illumina platforms.  Default: 33.
+.HP
+\fB\-r\fR, \fB\-\-read\-len\fR=\fI\,LEN\/\fR
+.HP
+\fB\-f\fR, \fB\-\-fragment\-len\fR=\fI\,LEN\/\fR
+.TP
+\fB\-s\fR, \fB\-\-fragment\-len\-stddev\fR=\fI\,LEN\/\fR
+Average read length, fragment length, and fragment
+standard deviation.  These are convenience parameters
+only, as they are only used for calculating the
+maximum overlap (\fB\-\-max\-overlap\fR) parameter.
+The maximum overlap is calculated as the overlap of
+average\-length reads from an average\-size fragment
+plus 2.5 times the fragment length standard
+deviation.  The default values are \fB\-r\fR 100, \fB\-f\fR 180,
+and \fB\-s\fR 18, so this works out to a maximum overlap of
+65 bp.  If \fB\-\-max\-overlap\fR is specified, then the
+specified value overrides the calculated value.
+.TP
+If you do not know the standard deviation of the
+fragment library, you can probably assume that the
+standard deviation is 10% of the average fragment
+length.
+.TP
+\fB\-\-cap\-mismatch\-quals\fR
+Cap quality scores assigned at mismatch locations
+to 2.  This was the default behavior in FLASH v1.2.7
+and earlier.  Later versions will instead calculate
+such scores as max(|q1 \- q2|, 2); that is, the
+absolute value of the difference in quality scores,
+but at least 2.  Essentially, the new behavior
+prevents a low quality base call that is likely a
+sequencing error from significantly bringing down
+the quality of a high quality, likely correct base
+call.
+.TP
+\fB\-\-interleaved\-input\fR
+Instead of requiring files MATES_1.FASTQ and
+MATES_2.FASTQ, allow a single file MATES.FASTQ that
+has the paired\-end reads interleaved.  Specify "\-"
+to read from standard input.
+.TP
+\fB\-\-interleaved\-output\fR
+Write the uncombined pairs in interleaved FASTQ
+format.
+.TP
+\fB\-I\fR, \fB\-\-interleaved\fR
+Equivalent to specifying both \fB\-\-interleaved\-input\fR
+and \fB\-\-interleaved\-output\fR.
+.TP
+\fB\-Ti\fR, \fB\-\-tab\-delimited\-input\fR
+Assume the input is in tab\-delimited format
+rather than FASTQ, in the format described below in
+\&'\-\-tab\-delimited\-output'.  In this mode you should
+provide a single input file, each line of which must
+contain either a read pair (5 fields) or a single
+read (3 fields).  FLASH will try to combine the read
+pairs.  Single reads will be written to the output
+file as\-is if also using \fB\-\-tab\-delimited\-output\fR;
+otherwise they will be ignored.  Note that you may
+specify "\-" as the input file to read the
+tab\-delimited data from standard input.
+.TP
+\fB\-To\fR, \fB\-\-tab\-delimited\-output\fR
+Write output in tab\-delimited format (not FASTQ).
+Each line will contain either a combined pair in the
+format 'tag <tab> seq <tab> qual' or an uncombined
+pair in the format 'tag <tab> seq_1 <tab> qual_1
+<tab> seq_2 <tab> qual_2'.
+.TP
+\fB\-o\fR, \fB\-\-output\-prefix\fR=\fI\,PREFIX\/\fR
+Prefix of output files.  Default: "out".
+.TP
+\fB\-d\fR, \fB\-\-output\-directory\fR=\fI\,DIR\/\fR
+Path to directory for output files.  Default:
+current working directory.
+.TP
+\fB\-c\fR, \fB\-\-to\-stdout\fR
+Write the combined reads to standard output.  In
+this mode, with FASTQ output (the default) the
+uncombined reads are discarded.  With tab\-delimited
+output, uncombined reads are included in the
+tab\-delimited data written to standard output.
+In both cases, histogram files are not written,
+and informational messages are sent to standard
+error rather than to standard output.
+.TP
+\fB\-z\fR, \fB\-\-compress\fR
+Compress the output files directly with zlib,
+using the gzip container format.  Similar to
+specifying \fB\-\-compress\-prog\fR=\fI\,gzip\/\fR and \fB\-\-suffix\fR=\fI\,gz\/\fR,
+but may be slightly faster.
+.TP
+\fB\-\-compress\-prog\fR=\fI\,PROG\/\fR
+Pipe the output through the compression program
+PROG, which will be called as `PROG \fB\-c\fR \-',
+plus any arguments specified by \fB\-\-compress\-prog\-args\fR.
+PROG must read uncompressed data from standard input
+and write compressed data to standard output when
+invoked as noted above.
+Examples: gzip, bzip2, xz, pigz.
+.TP
+\fB\-\-compress\-prog\-args\fR=\fI\,ARGS\/\fR
+A string of additional arguments that will be passed
+to the compression program if one is specified with
+\fB\-\-compress\-prog\fR=\fI\,PROG\/\fR.  (The arguments '\-c \-' are
+still passed in addition to explicitly specified
+arguments.)
+.TP
+\fB\-\-suffix\fR=\fI\,SUFFIX\/\fR, \fB\-\-output\-suffix\fR=\fI\,SUFFIX\/\fR
+Use SUFFIX as the suffix of the output files
+after ".fastq".  A dot before the suffix is assumed,
+unless an empty suffix is provided.  Default:
+nothing; or 'gz' if \fB\-z\fR is specified; or PROG if
+\fB\-\-compress\-prog\fR=\fI\,PROG\/\fR is specified.
+.TP
+\fB\-t\fR, \fB\-\-threads\fR=\fI\,NTHREADS\/\fR
+Set the number of worker threads.  This is in
+addition to the I/O threads.  Default: number of
+processors.  Note: if you need FLASH's output to
+appear deterministically or in the same order as
+the original reads, you must specify \fB\-t\fR 1
+(\fB\-\-threads\fR=\fI\,1\/\fR).
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Do not print informational messages.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Display this help and exit.
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Display version.
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/rules
=====================================
@@ -1,31 +1,12 @@
 #!/usr/bin/make -f
 
 # DH_VERBOSE := 1
-export LC_ALL=C.UTF-8
-
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
 
 # for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
 	dh $@
 
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
-#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-#	do_stuff_for_testing
-#endif
-
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-#	. debian/get-orig-source
+override_dh_installchangelogs:
+	dh_installchangelogs NEWS



View it on GitLab: https://salsa.debian.org/med-team/flash/-/compare/528e472a036f75252b01eaf2bf1007b3b6b95dd8...36402d4b8b1403feda8aae690bc4b3f2f6bca83e

-- 
View it on GitLab: https://salsa.debian.org/med-team/flash/-/compare/528e472a036f75252b01eaf2bf1007b3b6b95dd8...36402d4b8b1403feda8aae690bc4b3f2f6bca83e
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