.gitignore

+*.pyc
+.*.swp
+build/
+dist/
+pbalign.egg-info/
+.DS_Store

MANIFEST.in

+include LICENSES.txt

Makefile

@@ -15,10 +15,13 @@ install:
 develop:
 	python setup.py develop
 
-test:
+pylint:
+	pylint --errors-only pbalign
+
+test: pylint
 	# Unit tests
 	#find tests/unit -name "*.py" | xargs nosetests
-	nosetests --verbose tests/unit/*.py
+	python setup.py test
 	# End-to-end tests
 	@echo pbalign cram tests require blasr installed.
 	find tests/cram -name "*.t" | xargs cram 

README.md

@@ -3,3 +3,7 @@ pbalign maps PacBio reads to reference sequences.
 Want to know how to install and run pbalign?
 
 Please refer to https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst
+
+DISCLAIMER
+----------
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

bamboo_build.sh

+#!/usr/bin/env bash
+set -vex
+
+################
+# DEPENDENCIES #
+################
+
+## Load modules
+type module >& /dev/null || . /mnt/software/Modules/current/init/bash
+
+module purge
+
+module load gcc
+module load git
+module load samtools
+
+module load python/2
+
+case "${bamboo_planRepository_branchName}" in
+  master)
+    module load blasr/master
+    ;;
+  *)
+    module load blasr/develop
+    ;;
+esac
+
+
+rm -rf prebuilts build
+test -d .pip/wheels && find .pip/wheels -type f ! -name '*none-any.whl' -print -delete || true
+
+export NX3PBASEURL=http://nexus/repository/unsupported/pitchfork/gcc-6.4.0
+export PATH="${PWD}/build/bin:${PATH}"
+export PYTHONUSERBASE="${PWD}/build"
+export PIP="pip --cache-dir=$bamboo_build_working_directory/.pip"
+
+CUR_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+source "${CUR_DIR}"/scripts/ci/build.sh
+source "${CUR_DIR}"/scripts/ci/test.sh

debian/changelog

+pbalign (0.3.1-1) unstable; urgency=medium
+
+  * Team upload.
+  * Add watch file
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Testsuite: autopkgtest-pkg-python
+  * Secure URI in copyright format
+  * Remove trailing whitespace in debian/control
+  * Build-Depends: s/python-sphinx/python3-sphinx/
+  * pbalign versioned depends: python-pbalign (= ${source:Version})
+  * Create manpages before building package
+
+ -- Andreas Tille <tille@debian.org>  Wed, 31 Oct 2018 07:53:41 +0100
+
 pbalign (0.3.0-1) unstable; urgency=medium
 
   * New upstream release (corresponds to smrtanalysis-4.0.0 tag)

debian/compat

-9
+11

debian/control

 Source: pbalign
-Section: python
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Afif Elghraoui <afif@debian.org>
-Build-Depends:
-	debhelper (>= 9),
+Section: python
+Testsuite: autopkgtest-pkg-python
+Priority: optional
+Build-Depends: debhelper (>= 11~),
                dh-python,
                python-all,
                python-setuptools,
-	python-pbcore (>= 0.8.5),
-	python-pbcommand (>= 0.2.0),
-	python-sphinx,
-	help2man,
-Standards-Version: 3.9.8
+               python-pbcore,
+               python-pbcommand,
+               python3-sphinx,
+               python-nose
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/pbalign
+Vcs-Git: https://salsa.debian.org/med-team/pbalign.git
 Homepage: https://github.com/PacificBiosciences/pbalign
-Vcs-Git: https://anonscm.debian.org/git/debian-med/pbalign.git
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbalign.git
 
 Package: pbalign
 Architecture: all
-Depends:
-	${misc:Depends},
+Depends: ${misc:Depends},
          ${python:Depends},
-	python-pbalign,
+         python-pbalign (= ${source:Version}),
          python-pkg-resources,
-	blasr (>= 5.3+0),
-Recommends:
-	python-pbh5tools,
-	hdf5-tools,
-Suggests:
-	bowtie2,
+         blasr (>= 5.3+0)
+Recommends: python-pbh5tools,
+            hdf5-tools
+Suggests: bowtie2,
           gmap,
-	pbalign-doc,
+          pbalign-doc
 Description: map Pacific Biosciences reads to reference DNA sequences
  pbalign aligns PacBio reads to reference sequences, filters aligned
  reads according to user-specific filtering criteria, and converts the
@@ -42,17 +39,14 @@ Description: map Pacific Biosciences reads to reference DNA sequences
 
 Package: python-pbalign
 Architecture: all
-Depends:
-	${misc:Depends},
+Depends: ${misc:Depends},
          ${python:Depends},
-	blasr (>= 5.3+0),
-Recommends:
-	python-pbh5tools,
-	hdf5-tools,
-Suggests:
-	bowtie2,
+         blasr (>= 5.3+0)
+Recommends: python-pbh5tools,
+            hdf5-tools
+Suggests: bowtie2,
           gmap,
-	pbalign-doc,
+          pbalign-doc
 Description: map Pacific Biosciences reads to reference DNA sequences (Python2)
  pbalign aligns PacBio reads to reference sequences, filters aligned
  reads according to user-specific filtering criteria, and converts the
@@ -63,12 +57,11 @@ Description: map Pacific Biosciences reads to reference DNA sequences (Python2)
  Python library backend.
 
 Package: pbalign-doc
-Section: doc
 Architecture: all
-Depends:
-	${misc:Depends},
+Section: doc
+Depends: ${misc:Depends},
          libjs-jquery,
-	libjs-underscore,
+         libjs-underscore
 Description: documentation for pbalign
  pbalign aligns PacBio reads to reference sequences, filters aligned
  reads according to user-specific filtering criteria, and converts the

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: pbalign
 Upstream-Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
 Source: https://github.com/PacificBiosciences/pbalign

debian/createmanpages

+#!/bin/sh
+MANDIR=debian/mans
+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\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr  \
+         --name="Mapping PacBio sequences to references" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=createChemistryHeader
+help2man --no-info --no-discard-stderr \
+         --name="Create a SAM header with PacBio sequencing chemistry information" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=extractUnmappedSubreads
+help2man --no-info --no-discard-stderr \
+         --name="Extract unmapped subreads from a fasta file" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=loadChemistry
+help2man --no-info --no-discard-stderr \
+         --name="Load PacBio sequencing chemistry information" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=maskAlignedReads
+help2man --no-info --no-discard-stderr \
+         --name="Mask aligned reads in regions file" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+rm -f $MANDIR/*.py.1
+for man in $MANDIR/*.1 ; do
+    ln -s `basename $man` $MANDIR/`basename $man .1`.py.1
+done
+
+echo "$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/manpages

+debian/mans/*.1

debian/mans/createChemistryHeader.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH CREATECHEMISTRYHEADER "1" "October 2018" "createChemistryHeader 0.3.1" "User Commands"
+.SH NAME
+createChemistryHeader \- Create a SAM header with PacBio sequencing chemistry information
+.SH DESCRIPTION
+usage: getChemistryHeader.py [\-h] [\-\-debug] \fB\-\-bas_files\fR BAS_FILES
+.TP
+[BAS_FILES ...]
+input_alignment_file output_header_file
+.PP
+createChemistryHeader creates a SAM header that contains the chemistry
+information used by Quiver.
+.SS "positional arguments:"
+.TP
+input_alignment_file
+A SAM or BAM file produced by BLASR.
+.TP
+output_header_file
+Name of the SAM or BAM header file that will be
+created with chemistry information loaded.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-debug\fR
+Output detailed log information. (default: False)
+.TP
+\fB\-\-bas_files\fR BAS_FILES [BAS_FILES ...]
+The bas or bax files containing the reads that were
+aligned in the input_alignment_file. Also can be a
+fofn of bas or bax files. (default: None)
+.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/mans/createChemistryHeader.py.1

+createChemistryHeader.1
\ No newline at end of file

debian/mans/extractUnmappedSubreads.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH EXTRACTUNMAPPEDSUBREADS "1" "October 2018" "extractUnmappedSubreads 0.3.1" "User Commands"
+.SH NAME
+extractUnmappedSubreads \- Extract unmapped subreads from a fasta file
+.SH DESCRIPTION
+usage: extractUnmappedSubreads [\-h] [\-\-verbose] [\-\-version] [\-\-profile]
+.TP
+[\-\-debug]
+fasta cmp.h5 [cmp.h5 ...]
+.PP
+Extract unmapped subreads from a fasta file.
+.SS "positional arguments:"
+.TP
+fasta
+a fasta file containing all subreads.
+.TP
+cmp.h5
+input cmp.h5 files.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-verbose\fR, \fB\-v\fR
+Set the verbosity level (default: None)
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-profile\fR
+Print runtime profile at exit (default: False)
+.TP
+\fB\-\-debug\fR
+Catch exceptions in debugger (requires ipdb) (default: False)
+.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/mans/extractUnmappedSubreads.py.1

+extractUnmappedSubreads.1
\ No newline at end of file

debian/mans/loadChemistry.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH LOADCHEMISTRY "1" "October 2018" "loadChemistry 0.3.1" "User Commands"
+.SH NAME
+loadChemistry \- Load PacBio sequencing chemistry information
+.SH DESCRIPTION
+loadChemistry.py
+.TP
+Load chemistry info into a cmp.h5, just copying the triple.
+Note
+.IP
+that there is no attempt to "decode" chemistry barcodes here\-\-\-this
+is a dumb pipe.
+.IP
+usage:
+.IP
+\f(CW% loadChemistry [input.fofn | list of input.ba[sx].h5] aligned_reads.cmp.h5\fR
+.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/mans/loadChemistry.py.1

+loadChemistry.1
\ No newline at end of file

debian/mans/maskAlignedReads.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH MASKALIGNEDREADS "1" "October 2018" "maskAlignedReads 0.3.1" "User Commands"
+.SH NAME
+maskAlignedReads \- Mask aligned reads in regions file
+.SH DESCRIPTION
+usage: maskAlignedReads [\-h] [\-v] [\-l LOGFILE] [\-d] [\-i]
+.IP
+inCmpFile inRgnFofn outRgnFofn
+.PP
+Use in.cmp.h5 to mask corresponding regions of files in in.rgn.h5, write output
+to a new rgn.fofn.
+.SS "positional arguments:"
+.TP
+inCmpFile
+An input cmp.h5 file.
+.TP
+inRgnFofn
+A fofn of input region table files.
+.TP
+outRgnFofn
+A fofn of output region table files.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-l\fR LOGFILE, \fB\-\-logFile\fR LOGFILE
+Specify a file to log to. Defaults to stderr.
+(default: None)
+.TP
+\fB\-d\fR, \fB\-\-debug\fR
+Increases verbosity of logging (default: False)
+.TP
+\fB\-i\fR, \fB\-\-info\fR
+Display informative log entries (default: False)
+.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/mans/maskAlignedReads.py.1

+maskAlignedReads.1
\ No newline at end of file

debian/mans/pbalign.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH PBALIGN "1" "October 2018" "pbalign 0.3.1" "User Commands"
+.SH NAME
+pbalign \- Mapping PacBio sequences to references
+.SH DESCRIPTION
+usage: pbalign [\-h] [\-\-version] [\-\-log\-file LOG_FILE]
+.IP
+[\-\-log\-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | \fB\-\-debug\fR | \fB\-\-quiet\fR | \fB\-v]\fR
+[\-\-pdb] [\-\-regionTable REGIONTABLE] [\-\-configFile CONFIGFILE]
+[\-\-pulseFile PULSEFILE] [\-\-algorithm {blasr,bowtie,gmap}]
+[\-\-maxHits MAXHITS] [\-\-minAnchorSize MINANCHORSIZE]
+[\-\-maxMatch MAXMATCH]
+[\-\-useccs {useccs,useccsall,useccsdenovo}] [\-\-noSplitSubreads]
+[\-\-concordant] [\-\-nproc NPROC]
+[\-\-algorithmOptions ALGORITHMOPTIONS]
+[\-\-maxDivergence MAXDIVERGENCE] [\-\-minAccuracy MINACCURACY]
+[\-\-minLength MINLENGTH] [\-\-scoreCutoff SCORECUTOFF]
+[\-\-hitPolicy {randombest,allbest,random,all,leftmost}]
+[\-\-filterAdapterOnly] [\-\-unaligned UNALIGNED] [\-\-seed SEED]
+[\-\-tmpDir TMPDIR] [\-\-profile]
+inputFileName referencePath outputFileName
+.PP
+Mapping PacBio sequences to references using an algorithm selected from a
+selection of supported command\-line alignment algorithms. Input can be a
+fasta, pls.h5, bas.h5 or ccs.h5 file or a fofn (file of file names). Output
+can be in SAM or BAM format. If output is BAM format, aligner can only be
+blasr and QVs will be loaded automatically. NOTE that pbalign no longer
+supports CMP.H5 in 3.0.
+.SS "positional arguments:"
+.TP
+inputFileName
+SubreadSet or unaligned .bam
+.TP
+referencePath
+Reference DataSet or FASTA file
+.TP
+outputFileName
+Alignment results dataset
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-log\-file\fR LOG_FILE
+Write the log to file. Default(None) will write to
+stdout. (default: None)
+.TP
+\fB\-\-log\-level\fR {DEBUG,INFO,WARNING,ERROR,CRITICAL}
+Set log level (default: INFO)
+.TP
+\fB\-\-debug\fR
+Alias for setting log level to DEBUG (default: False)
+.TP
+\fB\-\-quiet\fR
+Alias for setting log level to CRITICAL to suppress
+output. (default: False)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Set the verbosity level. (default: None)
+.TP
+\fB\-\-pdb\fR
+Enable Python debugger (default: False)
+.TP
+\fB\-\-profile\fR
+Print runtime profile at exit (default: False)
+.SS "Optional input arguments:"
+.TP
+\fB\-\-regionTable\fR REGIONTABLE
+Specify a region table for filtering reads. (default:
+None)
+.TP
+\fB\-\-configFile\fR CONFIGFILE
+Specify a set of user\-defined argument values.
+(default: None)
+.TP
+\fB\-\-pulseFile\fR PULSEFILE
+When input reads are in fasta format and output is a
+cmp.h5 this option can specify pls.h5 or bas.h5 or
+FOFN files from which pulse metrics can be loaded for
+Quiver. (default: None)
+.SS "Alignment options:"
+.TP
+\fB\-\-algorithm\fR {blasr,bowtie,gmap}
+Select an aligorithm from ('blasr', 'bowtie', 'gmap').
+(default: blasr)
+.TP
+\fB\-\-maxHits\fR MAXHITS
+The maximum number of matches of each read to the
+reference sequence that will be evaluated. (default:
+None)
+.TP
+\fB\-\-minAnchorSize\fR MINANCHORSIZE
+The minimum anchor size defines the length of the read
+that must match against the reference sequence.
+(default: None)
+.TP
+\fB\-\-maxMatch\fR MAXMATCH
+BLASR maxMatch option. (Will be overridden if is also
+set in algorithmOptions) (default: 30)
+.TP
+\fB\-\-useccs\fR {useccs,useccsall,useccsdenovo}
+Map the ccsSequence to the genome first, then align
+subreads to the interval that the CCS reads mapped to.
+useccs: only maps subreads that span the length of the
+template. useccsall: maps all subreads. useccsdenovo:
+maps ccs only. (default: None)
+.TP
+\fB\-\-noSplitSubreads\fR
+Do not split reads into subreads even if subread
+regions are available. (default: False)
+.TP
+\fB\-\-concordant\fR
+Map subreads of a ZMW to the same genomic location.
+(default: False)
+.TP
+\fB\-\-nproc\fR NPROC
+Number of threads. (default: 8)
+.TP
+\fB\-\-algorithmOptions\fR ALGORITHMOPTIONS
+Pass alignment options through. (default: None)
+.SS "Filter criteria options:"
+.TP
+\fB\-\-maxDivergence\fR MAXDIVERGENCE
+The maximum allowed percentage divergence of a read
+from the reference sequence. (default: 30.0)
+.TP
+\fB\-\-minAccuracy\fR MINACCURACY
+The minimum concordance of alignments that will be
+evaluated. (default: 70.0)
+.TP
+\fB\-\-minLength\fR MINLENGTH
+The minimum aligned read length of alignments that
+will be evaluated. (default: 50)
+.TP
+\fB\-\-scoreCutoff\fR SCORECUTOFF
+The worst score to output an alignment. (default:
+None)
+.TP
+\fB\-\-hitPolicy\fR {randombest,allbest,random,all,leftmost}
+Specify a policy for how to treat multiple hit random
+: selects a random hit. all : selects all hits.
+allbest : selects all the best score hits. randombest:
+selects a random hit from all best score hits.
+leftmost : selects a hit which has the best score and
+the smallest mapping coordinate in any reference.
+(default: randombest)
+.TP
+\fB\-\-filterAdapterOnly\fR
+If specified, do not report adapter\-only hits using
+annotations with the reference entry. (default: False)
+.SS "Miscellaneous options:"
+.TP
+\fB\-\-unaligned\fR UNALIGNED
+Output names of unaligned reads to specified file.
+(default: None)
+.TP
+\fB\-\-seed\fR SEED
+Initialize the random number generator with a nonezero integer. Zero means that current system time is
+used. (default: 1)
+.TP
+\fB\-\-tmpDir\fR TMPDIR
+Specify a directory for saving temporary files.
+(default: \fI\,/tmp\/\fP)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.