[med-svn] [blasr] 02/02: Add draft man pages generated by help2man

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch master
in repository blasr.

commit fb596d81b977d0c09bfa831ae0301b0c8c68e5a1
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Jul 29 00:17:35 2015 -0700

    Add draft man pages generated by help2man
    
    blasr has two pages since the -help and -h flags on the binary
    have different outputs. One is an explanation of how to use it
    while the other is a summary of options available. These two need
    to be combined into one manpage.
---
 debian/blasr.1.first  |  70 +++++++++
 debian/blasr.1.second | 385 ++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/loadPulses.1   |  72 ++++++++++
 debian/pls2fasta.1    |  76 ++++++++++
 debian/samFilter.1    | 130 +++++++++++++++++
 debian/samtoh5.1      |  56 ++++++++
 debian/samtom4.1      |  29 ++++
 debian/sawriter.1     |  39 +++++
 debian/sdpMatcher.1   |   6 +
 debian/toAfg.1        |  14 ++
 10 files changed, 877 insertions(+)

diff --git a/debian/blasr.1.first b/debian/blasr.1.first
new file mode 100644
index 0000000..ce4a776
--- /dev/null
+++ b/debian/blasr.1.first
@@ -0,0 +1,70 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH BLASR "1" "July 2015" "blasr git1dlkf23" "User Commands"
+.SH NAME
+blasr \- program description goes here
+.SH DESCRIPTION
+NAME
+.IP
+blasr \- Map SMRT Sequences to a reference genome.
+.PP
+SYNOPSIS
+.IP
+blasr reads.bam genome.fasta \fB\-bam\fR \fB\-out\fR out.bam
+.IP
+blasr reads.fasta genome.fasta
+.IP
+blasr reads.fasta genome.fasta \fB\-sa\fR genome.fasta.sa
+.IP
+blasr reads.bax.h5 genome.fasta [\-sa genome.fasta.sa]
+.IP
+blasr reads.bax.h5 genome.fasta \fB\-sa\fR genome.fasta.sa \fB\-maxScore\fR \fB\-100\fR \fB\-minMatch\fR 15 ...
+.IP
+blasr reads.bax.h5 genome.fasta \fB\-sa\fR genome.fasta.sa \fB\-nproc\fR 24 \fB\-out\fR alignment.out ...
+.PP
+DESCRIPTION
+.IP
+blasr is a read mapping program that maps reads to positions
+in a genome by clustering short exact matches between the read and
+the genome, and scoring clusters using alignment. The matches are
+generated by searching all suffixes of a read against the genome
+using a suffix array. Global chaining methods are used to score
+clusters of matches.
+.IP
+The only required inputs to blasr are a file of reads and a
+reference genome.  It is exremely useful to have read filtering
+information, and mapping runtime may decrease substantially when a
+precomputed suffix array index on the reference sequence is
+specified.
+.IP
+Although reads may be input in FASTA format, the recommended input is
+PacBio BAM files because these contain qualtiy value
+information that is used in the alignment and produces higher quality
+variant detection.
+Although alignments can be output in various formats, the recommended
+output format is PacBio BAM.
+Support to bax.h5 and plx.h5 files will be DEPRECATED.
+Support to region tables for h5 files will be DEPRECATED.
+.IP
+When suffix array index of a genome is not specified, the suffix array is
+built before producing alignment.   This may be prohibitively slow
+when the genome is large (e.g. Human).  It is best to precompute the
+suffix array of a genome using the program sawriter, and then specify
+the suffix array on the command line using \fB\-sa\fR genome.fa.sa.
+.IP
+The optional parameters are roughly divided into three categories:
+control over anchoring, alignment scoring, and output.
+.IP
+The default anchoring parameters are optimal for small genomes and
+samples with up to 5% divergence from the reference genome.  The main
+parameter governing speed and sensitivity is the \fB\-minMatch\fR parameter.
+For human genome alignments, a value of 11 or higher is recommended.
+Several methods may be used to speed up alignments, at the expense of
+possibly decreasing sensitivity.
+.IP
+Regions that are too repetitive may be ignored during mapping by
+limiting the number of positions a read maps to with the
+\fB\-maxAnchorsPerPosition\fR option.  Values between 500 and 1000 are effective
+in the human genome.
+.IP
+For small genomes such as bacterial genomes or BACs, the default parameters
+are sufficient for maximal sensitivity and good speed.
diff --git a/debian/blasr.1.second b/debian/blasr.1.second
new file mode 100644
index 0000000..ccee73e
--- /dev/null
+++ b/debian/blasr.1.second
@@ -0,0 +1,385 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH BLASR "1" "July 2015" "blasr git1dlkf23" "User Commands"
+.SH NAME
+blasr \- program description goes here
+.SH DESCRIPTION
+.IP
+Options for blasr
+Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [\-options]
+.IP
+option Description (default_value).
+.IP
+Input Files.
+.TP
+reads.bam
+is a PacBio BAM file of reads.
+This is the preferred input to blasr because rich quality
+value (insertion,deletion, and substitution quality values) information is
+maintained.  The extra quality information improves variant detection and mapping
+speed.
+.TP
+reads.fasta is a multi\-fasta file of reads.
+While any fasta file is valid input,
+.IP
+reads.bax.h5|reads.plx.h5 is the old DEPRECATED output format of SMRT reads.
+input.fofn  File of file names accepted.
+.HP
+\fB\-sa\fR suffixArrayFile
+.IP
+Use the suffix array 'sa' for detecting matches
+between the reads and the reference.  The suffix
+array has been prepared by the sawriter program.
+.HP
+\fB\-ctab\fR tab
+.TP
+A table of tuple counts used to estimate match significance.
+This is
+.TP
+by the program 'printTupleCountTable'.
+While it is quick to generate on
+.IP
+the fly, if there are many invocations of blasr, it is useful to
+precompute the ctab.
+.HP
+\fB\-regionTable\fR table (DEPRECATED)
+.IP
+Read in a read\-region table in HDF format for masking portions of reads.
+This may be a single table if there is just one input file,
+or a fofn.  When a region table is specified, any region table inside
+the reads.plx.h5 or reads.bax.h5 files are ignored.
+.PP
+(DEPRECATED) Options for modifying reads.
+.IP
+There is ancilliary information about substrings of reads
+that is stored in a 'region table' for each read file.  Because
+HDF is used, the region table may be part of the .bax.h5 or .plx.h5 file,
+or a separate file.  A contiguously read substring from the template
+is a subread, and any read may contain multiple subreads. The boundaries
+of the subreads may be inferred from the region table either directly or
+by definition of adapter boundaries.  Typically region tables also
+contain information for the location of the high and low quality regions of
+reads.  Reads produced by spurrious reads from empty ZMWs have a high
+quality start coordinate equal to high quality end, making no usable read.
+.HP
+\fB\-useccs\fR
+.IP
+Align the circular consensus sequence (ccs), then report alignments
+of the ccs subreads to the window that the ccs was mapped to.  Only
+alignments of the subreads are reported.
+.HP
+\fB\-useccsall\fR
+.IP
+Similar to \fB\-useccs\fR, except all subreads are aligned, rather than just
+the subreads used to call the ccs.  This will include reads that only
+cover part of the template.
+.HP
+\fB\-useccsdenovo\fR
+.IP
+Align the circular consensus, and report only the alignment of the ccs
+sequence.
+.HP
+\fB\-noSplitSubreads\fR (false)
+.TP
+Do not split subreads at adapters.
+This is typically only
+.IP
+useful when the genome in an unrolled version of a known template, and
+contains template\-adapter\-reverse_template sequence.
+.HP
+\fB\-ignoreRegions\fR(false)
+.IP
+Ignore any information in the region table.
+.HP
+\fB\-ignoreHQRegions\fR (false)Ignore any hq regions in the region table.
+.IP
+Alignments To Report.
+.HP
+\fB\-bestn\fR n (10)
+.IP
+Report the top 'n' alignments.
+.HP
+\fB\-hitPolicy\fR
+.IP
+(all) Specify a policy to treat multiple hits from [all, allbest, random, randombest, leftmost]
+.TP
+all
+: report all alignments.
+.TP
+allbest
+: report all equally top scoring alignments.
+.TP
+random
+: report a random alignment.
+.IP
+randombest: report a random alignment from multiple equally top scoring alignments.
+leftmost  : report an alignment which has the best alignmentscore and has the smallest mapping coordinate in any reference.
+.HP
+\fB\-placeRepeatsRandomly\fR (false)
+.IP
+DEPRECATED! If true, equivalent to \fB\-hitPolicy\fR randombest.
+.HP
+\fB\-randomSeed\fR (0)
+.IP
+Seed for random number generator. By default (0), use current time as seed.
+.HP
+\fB\-noSortRefinedAlignments\fR (false)
+.IP
+Once candidate alignments are generated and scored via sparse dynamic
+programming, they are rescored using local alignment that accounts
+for different error profiles.
+Resorting based on the local alignment may change the order the hits are returned.
+.HP
+\fB\-allowAdjacentIndels\fR
+.IP
+When specified, adjacent insertion or deletions are allowed. Otherwise, adjacent
+insertion and deletions are merged into one operation.  Using quality values
+to guide pairwise alignments may dictate that the higher probability alignment
+contains adjacent insertions or deletions.  Current tools such as GATK do not permit
+this and so they are not reported by default.
+.IP
+Output Formats and Files
+.HP
+\fB\-out\fR out (terminal)
+.IP
+Write output to 'out'.
+.TP
+\fB\-sam\fR
+Write output in SAM format.
+.HP
+\fB\-m\fR t
+.IP
+If not printing SAM, modify the output of the alignment.
+.IP
+t=0 Print blast like output with |'s connecting matched nucleotides.
+.IP
+1 Print only a summary: score and pos.
+2 Print in Compare.xml format.
+3 Print in vulgar format (DEPRECATED).
+4 Print a longer tabular version of the alignment.
+5 Print in a machine\-parsable format that is read by compareSequences.py.
+.HP
+\fB\-header\fR
+.IP
+Print a header as the first line of the output file describing the contents of each column.
+.HP
+\fB\-titleTable\fR tab (NULL)
+.TP
+Construct a table of reference sequence titles.
+The reference sequences are
+.TP
+enumerated by row, 0,1,...
+The reference index is printed in alignment results
+.TP
+rather than the full reference name.
+This makes output concise, particularly when
+.IP
+very verbose titles exist in reference names.
+.HP
+\fB\-unaligned\fR file
+.IP
+Output reads that are not aligned to 'file'
+.HP
+\fB\-clipping\fR [none|hard|subread|soft] (none)
+.IP
+Use no/hard/subread/soft clipping, ONLY for SAM/BAM output.
+.HP
+\fB\-printSAMQV\fR (false)
+.IP
+Print quality values to SAM output.
+.HP
+\fB\-cigarUseSeqMatch\fR (false)
+.IP
+CIGAR strings in SAM/BAM output use '=' and 'X' to represent sequence match and mismatch instead of 'M'.
+.IP
+Options for anchoring alignment regions. This will have the greatest effect on speed and sensitivity.
+.HP
+\fB\-minMatch\fR m (12)
+.TP
+Minimum seed length.
+Higher minMatch will speed up alignment,
+.IP
+but decrease sensitivity.
+.HP
+\fB\-maxMatch\fR l (inf)
+.IP
+Stop mapping a read to the genome when the lcp length reaches l.
+This is useful when the query is part of the reference, for example when
+constructing pairwise alignments for de novo assembly.
+.HP
+\fB\-maxLCPLength\fR l (inf)
+.IP
+The same as \fB\-maxMatch\fR.
+.HP
+\fB\-maxAnchorsPerPosition\fR m (10000)
+.IP
+Do not add anchors from a position if it matches to more than 'm' locations in the target.
+.HP
+\fB\-advanceExactMatches\fR E (0)
+.TP
+Another trick for speeding up alignments with match \- E fewer anchors.
+Rather than
+.IP
+finding anchors between the read and the genome at every position in the read,
+when an anchor is found at position i in a read of length L, the next position
+in a read to find an anchor is at i+L\-E.
+Use this when alignining already assembled contigs.
+.HP
+\fB\-nCandidates\fR n (10)
+.TP
+Keep up to 'n' candidates for the best alignment.
+A large value of n will slow mapping
+.IP
+because the slower dynamic programming steps are applied to more clusters of anchors
+which can be a rate limiting step when reads are very long.
+.HP
+\fB\-concordant\fR(false)
+.IP
+Map all subreads of a zmw (hole) to where the longest full pass subread of the zmw
+aligned to. This requires to use the region table and hq regions.
+This option only works when reads are in base or pulse h5 format.
+.HP
+\fB\-concordantTemplate\fR(mediansubread)
+.IP
+Select a full pass subread of a zmw as template for concordant mapping.
+longestsubread \- use the longest full pass subread
+mediansubread  \- use the median length full pass subread
+typicalsubread \- use the second longest full pass subread if length of
+.IP
+the longest full pass subread is an outlier
+.HP
+\fB\-fastMaxInterval\fR(false)
+.IP
+Fast search maximum increasing intervals as alignment candidates. The search
+is not as exhaustive as the default, but is much faster.
+.HP
+\fB\-aggressiveIntervalCut\fR(false)
+.IP
+Agreesively filter out non\-promising alignment candidates, if there
+exists at least one promising candidate. If this option is turned on,
+Blasr is likely to ignore short alignments of ALU elements.
+.HP
+\fB\-fastSDP\fR(false)
+.IP
+Use a fast heuristic algorithm to speed up sparse dynamic programming.
+.IP
+Options for Refining Hits.
+.HP
+\fB\-sdpTupleSize\fR K (11)
+.TP
+Use matches of length K to speed dynamic programming alignments.
+This controls
+.IP
+accuracy of assigning gaps in pairwise alignments once a mapping has been found,
+rather than mapping sensitivity itself.
+.HP
+\fB\-scoreMatrix\fR "score matrix string"
+.TP
+Specify an alternative score matrix for scoring fasta reads.
+The matrix is
+.IP
+in the format
+.IP
+ACGTN
+.IP
+A abcde
+C fghij
+G klmno
+T pqrst
+N uvwxy . The values a...y should be input as a quoted space separated
+.IP
+string: "a b c ... y". Lower scores are better, so matches should be less
+than mismatches e.g. a,g,m,s = \fB\-5\fR (match), mismatch = 6.
+.HP
+\fB\-affineOpen\fR value (10)
+.IP
+Set the penalty for opening an affine alignment.
+.HP
+\fB\-affineExtend\fR a (0)
+.IP
+Change affine (extension) gap penalty. Lower value allows more gaps.
+.IP
+Options for overlap/dynamic programming alignments and pairwise overlap for de novo assembly.
+.HP
+\fB\-useQuality\fR (false)
+.IP
+Use substitution/insertion/deletion/merge quality values to score gap and
+mismatch penalties in pairwise alignments.  Because the insertion and deletion
+rates are much higher than substitution, this will make many alignments
+favor an insertion/deletion over a substitution.  Naive consensus calling methods
+will then often miss substitution polymorphisms. This option should be
+used when calling consensus using the Quiver method.  Furthermore, when
+not using quality values to score alignments, there will be a lower consensus
+accuracy in homolymer regions.
+.HP
+\fB\-affineAlign\fR (false)
+.IP
+Refine alignment using affine guided align.
+.IP
+Options for filtering reads and alignments
+.HP
+\fB\-minReadLength\fR l(50)
+.IP
+Skip reads that have a full length less than l. Subreads may be shorter.
+.HP
+\fB\-minSubreadLength\fR l(0)
+.IP
+Do not align subreads of length less than l.
+.HP
+\fB\-minRawSubreadScore\fR m(0)
+.IP
+Do not align subreads whose quality score in region table is less than m (quality scores should be in range [0, 1000]).
+.HP
+\fB\-maxScore\fR m(\fB\-200\fR)
+.IP
+Maximum score to output (high is bad, negative good).
+.HP
+\fB\-minAlnLength\fR
+.IP
+(0) Report alignments only if their lengths are greater than minAlnLength.
+.HP
+\fB\-minPctSimilarity\fR
+.IP
+(0) Report alignments only if their percentage similairty is greater than minPctSimilarity.
+.HP
+\fB\-minPctAccuracy\fR
+.IP
+(0) Report alignments only if their percentage accuray is greater than minAccuracy.
+.IP
+Options for parallel alignment.
+.HP
+\fB\-nproc\fR N (1)
+.TP
+Align using N processes.
+All large data structures such as the suffix array and
+.IP
+tuple count table are shared.
+.HP
+\fB\-start\fR S (0)
+.IP
+Index of the first read to begin aligning. This is useful when multiple instances
+are running on the same data, for example when on a multi\-rack cluster.
+.HP
+\fB\-stride\fR S (1)
+.IP
+Align one read every 'S' reads.
+.IP
+Options for subsampling reads.
+.HP
+\fB\-subsample\fR (0)
+.IP
+Proportion of reads to randomly subsample (expressed as a decimal) and align.
+.HP
+\fB\-holeNumbers\fR LIST
+.IP
+When specified, only align reads whose ZMW hole numbers are in LIST.
+LIST is a comma\-delimited string of ranges, such as '1,2,3,10\-13'.
+This option only works when reads are in bam, bax.h5 or plx.h5 format.
+.TP
+\fB\-h\fR
+Print this help file.
+.PP
+To cite BLASR, please use: Chaisson M.J., and Tesler G., Mapping
+single molecule sequencing reads using Basic Local Alignment with
+Successive Refinement (BLASR): Theory and Application, BMC
+Bioinformatics 2012, 13:238.
+Please report any bugs to 'https://github.com/PacificBiosciences/blasr/issues'.
diff --git a/debian/loadPulses.1 b/debian/loadPulses.1
new file mode 100644
index 0000000..97bf857
--- /dev/null
+++ b/debian/loadPulses.1
@@ -0,0 +1,72 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH LOADPULSES "1" "July 2015" "loadPulses git1a3s3" "User Commands"
+.SH NAME
+loadPulses \- description of program
+.SH DESCRIPTION
+loadPulses Loads pulse information such as inter pulse distance, or quality
+.IP
+information into the cmp.h5 file. This allows one to analyze kinetic
+and quality information by alignment column.
+.PP
+usage: loadPulses basFileName cmpFileName [options]
+.IP
+basFileName
+.IP
+The input {bas,pls}.h5 or input.fofn.
+.IP
+cmpFileName
+.IP
+The cmp.h5 file to load pulse information into.
+.HP
+\fB\-metrics\fR value
+.IP
+A comma separated list of metrics (with no spaces).
+Valid options are:
+WhenStarted,QualityValue,InsertionQV,MergeQV,
+DeletionQV,DeletionTag,SubstitutionTag,SubstitutionQV,
+PreBaseFrames,IPD,StartFrame,PulseWidth,
+WidthInFrames,Light,pkmid,ClassifierQV,
+PulseIndex
+Default options are:
+QualityValue,ClassifierQV,StartFrame,PulseWidth,
+WidthInFrames,pkmid,IPD
+.HP
+\fB\-failOnMissingData\fR
+.IP
+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.
+.HP
+\fB\-byread\fR
+.IP
+Load pulse information by read rather than buffering metrics.
+.HP
+\fB\-bymetric\fR
+.IP
+Load pulse information by metric rather than by read. This uses
+more memory than \fB\-byread\fR, but can be faster.
+.HP
+\fB\-maxElements\fR value
+.IP
+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.
+.HP
+\fB\-maxMemory\fR value
+.IP
+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.
+.HP
+\fB\-metaNElements\fR value
+.IP
+Set number of elements in meta data cache for reading
+bas/bax/pls.h5 file.
+.HP
+\fB\-rawNElements\fR value
+.IP
+Set number of elements in raw data cache for reading
+bas/bax/pls.h5 file.
+.HP
+\fB\-rawChunkSize\fR value
+.IP
+Set chunk size of raw data cache for reading bas/bax/pls.h5
+file.
diff --git a/debian/pls2fasta.1 b/debian/pls2fasta.1
new file mode 100644
index 0000000..89df97d
--- /dev/null
+++ b/debian/pls2fasta.1
@@ -0,0 +1,76 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH PLS2FASTA "1" "July 2015" "pls2fasta git1a3s3" "User Commands"
+.SH NAME
+pls2fasta \- description of program
+.SH DESCRIPTION
+pls2fasta Converts plx.h5/bax.h5/fofn files to fasta or fastq files. Although
+.IP
+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.
+.PP
+usage: pls2fasta in.bax.h5 out.fasta [options]
+.IP
+in.bax.h5
+.IP
+Input plx.h5/bax.h5/fofn file.
+.IP
+out.fasta
+.IP
+Output fasta/fastq file.
+.HP
+\fB\-trimByRegion\fR
+.IP
+Trim away low quality regions.
+.HP
+\fB\-maskByRegion\fR
+.IP
+Mask low quality regions with 'N'.
+.HP
+\fB\-regionTable\fR value
+.IP
+Optional HDF file with a \fI\,/PulseData/Regions\/\fP dataset.
+.HP
+\fB\-minSubreadLength\fR value
+.IP
+Do not write subreads less than the specified length.
+.HP
+\fB\-noSplitSubreads\fR
+.IP
+Do not split reads on adapter sequences.
+.HP
+\fB\-holeNumber\fR
+.IP
+Only print this hole number (or list of numbers).
+.HP
+\fB\-fastq\fR
+.IP
+Print in FASTQ format with quality.
+.HP
+\fB\-ccs\fR
+.IP
+Print de novo CCS sequences
+.HP
+\fB\-lineLength\fR value
+.IP
+Specify fasta/fastq line length
+.HP
+\fB\-minReadScore\fR value
+.TP
+Minimum read score to print a read.
+The score is a number
+.IP
+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.
+.HP
+\fB\-best\fR
+.TP
+If a CCS sequence exists, print this.
+Otherwise, print the
+.TP
+longestsubread.
+This does not support fastq.
diff --git a/debian/samFilter.1 b/debian/samFilter.1
new file mode 100644
index 0000000..7eb9052
--- /dev/null
+++ b/debian/samFilter.1
@@ -0,0 +1,130 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SAMFILTER "1" "July 2015" "samFilter git1a3s3" "User Commands"
+.SH NAME
+samFilter \- description of program
+.SH DESCRIPTION
+usage:  [file.sam] [reference.fasta] [out.sam] [options]
+.IP
+file.sam
+.IP
+Input SAM file.
+.IP
+reference.fasta
+.IP
+Reference used to generate reads.
+.IP
+out.sam
+.IP
+Output SAM file.
+.HP
+\fB\-minAlnLength\fR value
+.IP
+(50) Report alignments only if their lengths are greater than
+minAlnLength.
+.HP
+\fB\-minAlignLength\fR value
+.IP
+Alias of \fB\-minAlnLength\fR
+.HP
+\fB\-minLength\fR value
+.IP
+Alias of \fB\-minAlnLength\fR
+.HP
+\fB\-minPctSimilarity\fR value
+.IP
+(70) Report alignments only if their percentage similairty is
+greater than minPctSimilarity.
+.HP
+\fB\-minPctIdentity\fR value
+.IP
+Alias of \fB\-minPctSimilarity\fR
+.HP
+\fB\-minPctAccuracy\fR value
+.IP
+(70) Report alignments only if their percentage accuray is
+greater than minAccuracy.
+.HP
+\fB\-minAccuracy\fR value
+.IP
+Alias of \fB\-minPctAccuracy\fR
+.HP
+\fB\-hitPolicy\fR value
+.IP
+(randombest) Specify a policy to treat multiple hits from [all,
+allbest, random, randombest, leftmost]
+.TP
+all
+: report all alignments.
+.TP
+allbest
+: report all equally top scoring alignments.
+.TP
+random
+: report a random alignment.
+.IP
+randombest: report a random alignment from multiple equally
+.IP
+top scoring alignments.
+.TP
+leftmost
+: report an alignment which has the best
+.IP
+alignmentscore and has the smallest mapping coordinate in any
+reference.
+.HP
+\fB\-scoreSign\fR value
+.IP
+(\fB\-1\fR) Whether higher or lower scores are better. \fB\-1\fR: lower is
+better; 1: higher is better.
+.HP
+\fB\-scoreCutoff\fR value
+.IP
+(INF) Report alignments only if their scores are no worse than
+score cut off.
+.HP
+\fB\-seed\fR value
+.TP
+(1)
+Seed for random number generator.
+.IP
+If seed is 0, then use current time as seed.
+.HP
+\fB\-holeNumbers\fR value
+.IP
+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.
+.HP
+\fB\-smrtTitle\fR
+.IP
+Use this option when filtering alignments generated by programs
+other than blasr, 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.
+.HP
+\fB\-titleTable\fR value
+.IP
+Use this experimental option when filtering alignments generated
+by blasr 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.
+.HP
+\fB\-filterAdapterOnly\fR value
+.IP
+Use this option to remove reads which can only map to adapters
+specified in the GFF file.
+.HP
+\fB\-v\fR
+.IP
+Be verbose.
+.IP
+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
+(blasr) it is defined as the start in the query sequence of the alignment.
+When "\-smrtTitle" 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.
diff --git a/debian/samtoh5.1 b/debian/samtoh5.1
new file mode 100644
index 0000000..00f967a
--- /dev/null
+++ b/debian/samtoh5.1
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SAMTOH5 "1" "July 2015" "samtoh5 git1a3s3" "User Commands"
+.SH NAME
+samtoh5 \- description of program
+.SH DESCRIPTION
+samtoh5 Converts in.sam file to out.cmp.h5 file.
+.PP
+usage: samtoh5 in.sam reference.fasta out.cmp.h5 [options]
+.IP
+in.sam
+.IP
+Input SAM file.
+.IP
+reference.fasta
+.IP
+Reference used to generate reads.
+.IP
+out.cmp.h5
+.IP
+Output cmp.h5 file.
+.HP
+\fB\-smrtTitle\fR
+.IP
+Use this option when converting alignments generated from reads
+produced by the pls2fasta 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.
+.HP
+\fB\-readType\fR value
+.IP
+Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA'
+.HP
+\fB\-verbosity\fR value
+.IP
+Set desired verbosity.
+.HP
+\fB\-useShortRefName\fR
+.IP
+Use abbreviated reference names obtained from file.sam instead
+of using full names from reference.fasta.
+.HP
+\fB\-copyQVs\fR
+.IP
+Copy all QVs available in the SAM file into the cmp.h5 file.
+This includes things like InsertionQV and DeletionTag.
+.IP
+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
+(blasr) it is defined as the start in the query sequence of the alignment.
+When "\-smrtTitle" 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.
diff --git a/debian/samtom4.1 b/debian/samtom4.1
new file mode 100644
index 0000000..05ffb6f
--- /dev/null
+++ b/debian/samtom4.1
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SAMTOM4 "1" "July 2015" "samtom4 git1a3s3" "User Commands"
+.SH NAME
+samtom4 \- description of program
+.SH DESCRIPTION
+samtom4 Converts a SAM file generated by blasr to M4 format.
+.PP
+usage: samtom4 [in.sam] [reference.fasta] [out.m4] [options]
+.IP
+in.sam
+.IP
+Input SAM file, which is produced by blasr.
+.IP
+reference.fasta
+.IP
+Reference used to generate file.sam.
+.IP
+out.m4
+.IP
+Output in blasr M4 format.
+.HP
+\fB\-header\fR
+.IP
+Print M4 header.
+.HP
+\fB\-useShortRefName\fR
+.IP
+Use abbreviated reference names obtained from file.sam instead
+of using full names from reference.fasta.
diff --git a/debian/sawriter.1 b/debian/sawriter.1
new file mode 100644
index 0000000..5defb7c
--- /dev/null
+++ b/debian/sawriter.1
@@ -0,0 +1,39 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SAWRITER "1" "July 2015" "sawriter git1a3s3" "User Commands"
+.SH NAME
+sawriter \- description of program
+.SH DESCRIPTION
+usage: sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [\-blt p] [\-larsson] [\-4bit] [\-manmy] [\-kar]
+.TP
+or
+sawriter fastaIn  (writes to fastIn.sa).
+\fB\-blt\fR p      Build a lookup table on prefixes of length 'p'. This speeds
+.IP
+up lookups considerably (more than the LCP table), but misses matches
+less than p when searching.
+.TP
+\fB\-4bit\fR
+Read in (one) fasta file as a compressed sequence file.
+.TP
+\fB\-larsson\fR
+(default)  Uses the method of Larsson and Sadakane to build the array.
+.TP
+\fB\-mamy\fR
+Uses the method of MAnber and MYers to build the array (slower than larsson,
+.IP
+and produces the same result. This is mainly for double checking
+the correctness of larsson).
+.TP
+\fB\-kark\fR
+Use Karkkainen DS3 method for building the suffix array.  This will probably be more
+slow than larsson, but takes only an extra N/(sqrt 3) extra space.
+.TP
+\fB\-mafe\fR
+(disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina
+.TP
+\fB\-welter\fR
+Use lightweight (sort of light) suffix array construction.  This is a bit more slow than
+normal larsson.
+.TP
+\fB\-welterweight\fR N use a difference cover of size N for building the suffix array.
+Valid values are 7,32,64,111, and 2281.
diff --git a/debian/sdpMatcher.1 b/debian/sdpMatcher.1
new file mode 100644
index 0000000..9fafd0a
--- /dev/null
+++ b/debian/sdpMatcher.1
@@ -0,0 +1,6 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SDPMATCHER "1" "July 2015" "sdpMatcher git1a3s3" "User Commands"
+.SH NAME
+sdpMatcher \- description of program
+.SH DESCRIPTION
+usage: sdpMatcher query target k [\-indelRate delta] [\-showalign] [\-printsw] [\-noRefine] [\-indel i] [ \fB\-local\fR ] [\-match m] [\-sdpIndel i]
diff --git a/debian/toAfg.1 b/debian/toAfg.1
new file mode 100644
index 0000000..b6f2678
--- /dev/null
+++ b/debian/toAfg.1
@@ -0,0 +1,14 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH TOAFG "1" "July 2015" "toAfg git1a3s3" "User Commands"
+.SH NAME
+toAfg \- description of program
+.SH DESCRIPTION
+usage: toAfg input.filetype output.filetype
+.TP
+[\-minSubreadLength l]
+[\-regionTable regions_file]
+[\-noSplitSubreads]
+[\-useccsdenovo]
+[\-uniformQV QV]
+.PP
+Print reads stored in a file (pls|fasta|fastq) as an afg.

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git