[med-svn] [Git][med-team/blasr][master] 7 commits: routine-update: debhelper-compat 13

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / blasr


Commits:
3305ef40 by Andreas Tille at 2021-04-17T23:26:05+02:00
routine-update: debhelper-compat 13

- - - - -
6f2450e5 by Andreas Tille at 2021-04-17T23:26:05+02:00
routine-update: Add salsa-ci file

- - - - -
e463122a by Andreas Tille at 2021-04-17T23:26:05+02:00
routine-update: Rules-Requires-Root: no

- - - - -
151edd01 by Andreas Tille at 2021-04-17T23:28:36+02:00
Set upstream metadata fields: Repository, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html

- - - - -
1581e460 by Andreas Tille at 2021-04-17T23:30:05+02:00
Versioned Build-Depends: libblasr-dev (>= 5.3.4+dfsg-3~) since other Debian releases put header file on wrong location

- - - - -
50e5ec64 by Andreas Tille at 2021-04-17T23:30:05+02:00
Remove old_manpages

- - - - -
81f260d9 by Andreas Tille at 2021-04-17T23:30:05+02:00
Upload to unstable

- - - - -


11 changed files:

- debian/changelog
- debian/control
- − debian/old_manpages/loadPulses.1
- − debian/old_manpages/pls2fasta.1
- − debian/old_manpages/samFilter.1
- − debian/old_manpages/samtoh5.1
- − debian/old_manpages/samtom4.1
- − debian/old_manpages/sdpMatcher.1
- − debian/old_manpages/toAfg.1
- + debian/salsa-ci.yml
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+blasr (5.3.3+dfsg-5) unstable; urgency=medium
+
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Repository, Repository-Browse.
+  * Versioned Build-Depends: libblasr-dev (>= 5.3.4+dfsg-3~) since other
+    Debian releases put header file on wrong location
+
+ -- Andreas Tille <tille at debian.org>  Mon, 16 Nov 2020 13:51:01 +0100
+
 blasr (5.3.3+dfsg-4) unstable; urgency=medium
 
   * Standards-Version: 4.5.0


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                python3,
                meson,
                cmake,
@@ -16,11 +16,12 @@ Build-Depends: debhelper-compat (= 12),
                libpbdata-dev,
                libpbcopper-dev,
                libgtest-dev,
-               libblasr-dev (>= 5.3.3+dfsg-2)
+               libblasr-dev (>= 5.3.4+dfsg-3~)
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/blasr
 Vcs-Git: https://salsa.debian.org/med-team/blasr.git
 Homepage: https://github.com/PacificBiosciences/blasr
+Rules-Requires-Root: no
 
 Package: blasr
 Architecture: any


=====================================
debian/old_manpages/loadPulses.1 deleted
=====================================
@@ -1,73 +0,0 @@
-.TH LOADPULSES "1" "July 2015" "loadPulses 3ca7fe8" "User Commands"
-.SH NAME
-loadPulses \- load sequencing pulse information
-.SH SYNOPSIS
-.B loadPulses
-.I basFileName
-.I cmpFileName
-.RI [ options ]
-.SH DESCRIPTION
-.B loadPulses
-loads sequencing pulse information such as inter-pulse distance or quality
-information into the cmp.h5 file.
-This allows one to analyze kinetic and quality information by alignment column.
-.SH OPTIONS
-.TP
-.I basFileName
-The input {bas,pls}.h5 or input.fofn.
-.TP
-.I cmpFileName
-The cmp.h5 file to load pulse information into.
-.TP
-.BI \-metrics \0value
-A comma separated list of metrics (with no spaces).
-.RS
-.TP
-Valid options are:
-WhenStarted, QualityValue, InsertionQV, MergeQV,
-DeletionQV, DeletionTag, SubstitutionTag, SubstitutionQV, PreBaseFrames, IPD,
-StartFrame, PulseWidth, WidthInFrames, Light, pkmid, ClassifierQV, PulseIndex
-.TP
-Default options are:
-QualityValue, ClassifierQV, StartFrame, PulseWidth,
-WidthInFrames, pkmid, IPD
-.RE
-.TP
-.B \-failOnMissingData
-Exit if any data fields are missing from the bas.h5 or pls.h5
-input that are required to load a metric. Defualt is a warning.
-.TP
-.B \-byread
-Load pulse information by read rather than buffering metrics.
-.TP
-.B \-bymetric
-Load pulse information by metric rather than by read. This uses
-more memory than \fB\-byread\fR, but can be faster.
-.TP
-.BI \-maxElements \0value
-Set a limit on the size of pls/bas file to buffer in with
-\fB\-bymetric\fR (default value: maximum int). Use \fB\-byread\fR if the limit
-is exceeded.
-.TP
-.BI \-maxMemory \0value
-Set a limit (in GB) on the memory to buffer data with \fB\-bymetric\fR
-(default value: 4 GB). Use \fB\-byread\fR if the limit is exceeded.
-.TP
-.BI \-metaNElements \0value
-Set number of elements in meta data cache for reading
-bas/bax/pls.h5 file.
-.TP
-.BI \-rawNElements value
-Set number of elements in raw data cache for reading the bas/bax/pls.h5 file.
-.TP
-.BI \-rawChunkSize \0value
-Set chunk size of raw data cache for reading the bas/bax/pls.h5 file.
-.SH SEE ALSO
-.BR blasr (1)
-.BR pls2fasta (1)
-.BR samFilter (1)
-.BR samtoh5 (1)
-.BR samtom4 (1)
-.BR sawriter (1)
-.BR sdpMatcher (1)
-.BR toAfg (1)


=====================================
debian/old_manpages/pls2fasta.1 deleted
=====================================
@@ -1,69 +0,0 @@
-.TH PLS2FASTA "1" "July 2015" "pls2fasta 3ca7fe8" "User Commands"
-.SH NAME
-pls2fasta \- convert plx.h5/bax.h5/fofn files to fasta or fastq files
-.SH SYNOPSIS
-.B pls2fasta
-.I in.bax.h5
-.I out.fasta
-.RI [ options ]
-.SH DESCRIPTION
-Although fasta files are provided with every run, they are not trimmed nor
-split into subreads. This program takes additional annotation
-information, such as the subread coordinates and high quality regions,
-and uses them to create fasta sequences that are substrings of all
-bases called. Most of the time, you will want to trim low quality
-reads, so you should specify \fB\-trimByRegion\fR.
-.SH OPTIONS
-.TP
-.I in.bax.h5
-Input plx.h5/bax.h5/fofn file.
-.TP
-.I out.fasta
-Output fasta/fastq file.
-.TP
-.B \-trimByRegion
-Trim away low quality regions.
-.TP
-.B \-maskByRegion
-Mask low quality regions with 'N'.
-.TP
-.BI \-regionTable \0value
-Optional HDF file with a \fI\,/PulseData/Regions\/\fP dataset.
-.TP
-.BI \-minSubreadLength \0value
-Do not write subreads less than the specified length.
-.TP
-.B \-noSplitSubreads
-Do not split reads on adapter sequences.
-.TP
-.B \-holeNumber
-Only print this hole number (or list of numbers).
-.TP
-.B \-fastq
-Print in FASTQ format with quality.
-.TP
-.B \-ccs
-Print de novo circular consensus (ccs) sequences
-.TP
-.B \-lineLength \0value
-Specify fasta/fastq line length
-.TP
-.BI \-minReadScore \0value
-Minimum read score to print a read.
-The score is a number between 0 and 1000 and represents the expected accuracy
-percentage * 10. A typical value would be between 750 and 800.
-This does not apply to ccs reads.
-.TP
-.B \-best
-If a ccs sequence exists, print this.
-Otherwise, print the longest subread.
-This does not support fastq.
-.SH SEE ALSO
-.BR blasr (1)
-.BR loadPulses (1)
-.BR samFilter (1)
-.BR samtoh5 (1)
-.BR samtom4 (1)
-.BR sawriter (1)
-.BR sdpMatcher (1)
-.BR toAfg (1)


=====================================
debian/old_manpages/samFilter.1 deleted
=====================================
@@ -1,134 +0,0 @@
-.TH SAMFILTER "1" "July 2015" "samFilter 3ca7fe8" "User Commands"
-.SH NAME
-samFilter \- filter nucleotide sequence alignments in SAM files
-.SH SYNOPSIS
-.B samFilter
-.I file.sam
-.I reference.fasta
-.I out.sam
-.RI [ options ]
-.SH OPTIONS
-.TP
-.I file.sam
-Input SAM file.
-.TP
-.I reference.fasta
-Reference used to generate reads.
-.TP
-.I out.sam
-Output SAM file.
-.TP
-.BI \-minAlnLength \0value
-(50) Report alignments only if their lengths are greater than
-\fIvalue\fR.
-.TP
-.BI \-minAlignLength \0value
-Alias of \fB\-minAlnLength\fR
-.TP
-.BI \-minLength \0value
-Alias of \fB\-minAlnLength\fR
-.TP
-.BI \-minPctSimilarity \0value
-.IP
-(70) Report alignments only if their percentage similairty is
-greater than \fIvalue\0.
-.TP
-.BI \-minPctIdentity \0value
-Alias of \fB\-minPctSimilarity\fR
-.TP
-.BI \-minPctAccuracy \0value
-(70) Report alignments only if their percentage accuray is
-greater than \fIvalue\fR.
-.TP
-.BI \-minAccuracy \0value
-Alias of \fB\-minPctAccuracy\fR
-.TP
-.BI \-hitPolicy \0value
-(randombest) Specify a policy to treat multiple hits from [all,
-allbest, random, randombest, leftmost]
-.RS
-.TP
-.I all
-report all alignments.
-.TP
-.I allbest
-report all equally top scoring alignments.
-.TP
-.I random
-report a random alignment.
-.TP
-.I randombest
-report a random alignment from multiple equally top scoring alignments.
-.TP
-.I leftmost
-report an alignment which has the best alignmentscore and has the smallest
-mapping coordinate in any reference.
-.RE
-.TP
-.BI \-scoreSign \0value
-(\-1) Whether higher or lower scores are better.
-.RS
-.TP
-\-1
-lower is better
-.TP
-1
-higher is better.
-.RE
-.TP
-.BI \-scoreCutoff \0value
-(INF) Report alignments only if their scores are no worse than
-\fIvalue\fR.
-.TP
-.BI \-seed \0value
-(1) Seed for random number generator.
-If seed is 0, then use current time as seed.
-.TP
-.BI \-holeNumbers \0value
-A string of comma-delimited hole number ranges to output hits,
-such as '1,2,10-12'. This requires hit titles to be in SMRT read
-title format.
-.TP
-.B \-smrtTitle
-Use this option when filtering alignments generated by programs
-other than
-.BR blasr (1),
-e.g. bwa\-sw or gmap. Parse read coordinates
-from the SMRT read title. The title is in the format
-\fI\,/name/hole/coordinates\/\fP, where coordinates are in the format
-\ed+_\ed+, and represent the interval of the read that was
-aligned.
-.TP
-.BI \-titleTable \0value
-Use this experimental option when filtering alignments generated
-by
-.BR blasr (1)
-with \fB\-titleTable\fR titleTableName, in which case
-reference titles in SAM are represented by their indices (e.g.,
-0, 1, 2, ...) in the title table.
-.TP
-.BI \-filterAdapterOnly \0value
-Use this option to remove reads which can only map to adapters
-specified in the GFF file.
-.TP
-.B \-v
-Be verbose.
-.SH NOTES
-Because SAM has optional tags that have different meanings in different
-programs, careful usage is required in order to have proper output.  The
-"xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM
-.RB ( blasr (1))
-it is defined as the start in the query sequence of the alignment.
-When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not
-specified, the coordinates given by the xs and xe tags are used to define
-the interval of a read that is aligned.  The CIGAR string is relative to
-this interval.
-.SH SEE ALSO
-.BR blasr (1)
-.BR loadPulses (1)
-.BR pls2fasta (1)
-.BR samtoh5 (1)
-.BR samtom4 (1)
-.BR sawriter (1)
-.BR sdpMatcher (1)
-.BR toAfg (1)


=====================================
debian/old_manpages/samtoh5.1 deleted
=====================================
@@ -1,62 +0,0 @@
-.TH SAMTOH5 "1" "July 2015" "samtoh5 3ca7fe8" "User Commands"
-.SH NAME
-samtoh5 \- convert a SAM file to cmp.h5 format
-.SH SYNOPSIS
-.B samtoh5 
-.I in.sam
-.I reference.fasta
-.I out.cmp.h5
-.RI [ options ]
-.SH OPTIONS
-.TP
-.I in.sam
-Input SAM file.
-.TP
-.I reference.fasta
-Reference used to generate reads.
-.TP
-.I out.cmp.h5
-Output cmp.h5 file.
-.TP
-.B \-smrtTitle
-Use this option when converting alignments generated from reads
-produced by the
-.BR pls2fasta (1)
-from bas.h5 files by parsing read
-coordinates from the SMRT read title. The title is in the
-format \fI\,/name/hole/coordinates\/\fP, where coordinates are in the
-format \ed+_\ed+, and represent the interval of the read that was
-aligned.
-.TP
-.BI \-readType \0value
-Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA'
-.TP
-.BI \-verbosity \0value
-Set desired verbosity.
-.TP
-.B \-useShortRefName
-Use abbreviated reference names obtained from \fIfile.sam\fR instead
-of using full names from \fIreference.fasta\fR.
-.TP
-.B \-copyQVs
-Copy all QVs available in the SAM file into the cmp.h5 file.
-This includes things like InsertionQV and DeletionTag.
-.SH NOTES
-Because SAM has optional tags that have different meanings in different
-programs, careful usage is required in order to have proper output. The
-"xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM
-.RB ( blasr (1))
-it is defined as the start in the query sequence of the alignment.
-When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not
-specified, the coordinates given by the xs and xe tags are used to define
-the interval of a read that is aligned. The CIGAR string is relative to
-this interval.
-.SH SEE ALSO
-.BR blasr (1)
-.BR loadPulses (1)
-.BR pls2fasta (1)
-.BR samFilter (1)
-.BR samtom4 (1)
-.BR sawriter (1)
-.BR sdpMatcher (1)
-.BR toAfg (1)


=====================================
debian/old_manpages/samtom4.1 deleted
=====================================
@@ -1,39 +0,0 @@
-.TH SAMTOM4 "1" "July 2015" "samtom4 3ca7fe8" "User Commands"
-.SH NAME
-samtom4 \- Convert a SAM file generated by
-.BR blasr (1)
-to M4 format
-.SH SYNOPSIS
-.B samtom4
-.I in.sam
-.I reference.fasta
-.I out.m4
-.RI [ options ]
-.SH OPTIONS
-.TP
-.I in.sam
-Input SAM file, which is produced by blasr.
-.TP
-.I reference.fasta
-Reference used to generate \fIfile.sam\fR.
-.TP
-.I out.m4
-Output in
-.BR blasr (1)
-M4 format.
-.TP
-.B \-header
-Print M4 header.
-.TP
-.B \-useShortRefName
-Use abbreviated reference names obtained from \fIfile.sam\fR instead
-of using full names from \fIreference.fasta\fR.
-.SH SEE ALSO
-.BR blasr (1)
-.BR loadPulses (1)
-.BR pls2fasta (1)
-.BR samFilter (1)
-.BR samtoh5 (1)
-.BR sawriter (1)
-.BR sdpMatcher (1)
-.BR toAfg (1)


=====================================
debian/old_manpages/sdpMatcher.1 deleted
=====================================
@@ -1,33 +0,0 @@
-.TH SDPMATCHER "1" "July 2015" "sdpMatcher 3ca7fe8" "User Commands"
-.SH NAME
-sdpMatcher \- nucleotide sequence matching using sparse dynamic programming
-.SH SYNOPSIS
-.B sdpMatcher
-.I query
-.I target
-.I k
-.RB [ \-indelRate
-.IR delta ]
-.RB [ \-showalign ]
-.RB [ \-printsw ]
-.RB [ \-noRefine ]
-.RB [ \-indel
-.IR i ]
-.RB [ \-local ]
-.RB [ \-match
-.IR m ]
-.RB [ \-sdpIndel
-.IR i ]
-.SH DESCRIPTION
-Performs sparse dynamic programming (SDP) between pairs of sequences as they 
-are given in two FASTA files, called \fIquery\fR and \fItarget\fR for
-convenience. \fIk\fR is the size of the k-mer used for the SDP algorithm..
-.SH SEE ALSO
-.BR blasr (1)
-.BR loadPulses (1)
-.BR pls2fasta (1)
-.BR samFilter (1)
-.BR samtoh5 (1)
-.BR samtom4 (1)
-.BR sawriter (1)
-.BR toAfg (1)


=====================================
debian/old_manpages/toAfg.1 deleted
=====================================
@@ -1,23 +0,0 @@
-.TH TOAFG "1" "July 2015" "toAfg 3ca7fe8" "User Commands"
-.SH NAME
-toAfg \- Print reads stored in a file (pls|fasta|fastq) as an afg.
-.SH SYNOPSIS
-.B toAfg
-.I input.filetype \0output.filetype
-.RB [ \-minSubreadLength
-.IR l ]
-.RB [ \-regionTable
-.IR regions_file ]
-.RB [ \-noSplitSubreads ]
-.RB [ \-useccsdenovo ]
-.RB [ \-uniformQV
-.IR QV ]
-.SH SEE ALSO
-.BR blasr (1)
-.BR loadPulses (1)
-.BR pls2fasta (1)
-.BR samFilter (1)
-.BR samtoh5 (1)
-.BR samtom4 (1)
-.BR sawriter (1)
-.BR sdpMatcher (1)


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/upstream/metadata
=====================================
@@ -21,3 +21,5 @@ Registry:
    Entry: blasr
  - Name: guix
    Entry: blasr
+Repository: https://github.com/PacificBiosciences/blasr.git
+Repository-Browse: https://github.com/PacificBiosciences/blasr



View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/4c589b7ececd465b94f63ec752897894ee6c483f...81f260d916c71b9d655dd3781a3b527d5cca0fa0

-- 
View it on GitLab: https://salsa.debian.org/med-team/blasr/-/compare/4c589b7ececd465b94f63ec752897894ee6c483f...81f260d916c71b9d655dd3781a3b527d5cca0fa0
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