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commit 7469d56e41efacb9ce8fc3f8d6523d861a32c204
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Sat May 23 01:43:24 2015 -0700
Draft manpages generated with help2man
These are not for all the executables. Some of
them have no usage information, so I assume that
they are for internal use only.
---
debian/existDB.1 | 51 +++++++++++
debian/kmer-mask.1 | 69 ++++++++++++++
debian/mapMers-depth.1 | 28 ++++++
debian/mapMers.1 | 7 ++
debian/meryl.1 | 242 +++++++++++++++++++++++++++++++++++++++++++++++++
debian/positionDB.1 | 67 ++++++++++++++
6 files changed, 464 insertions(+)
diff --git a/debian/existDB.1 b/debian/existDB.1
new file mode 100644
index 0000000..36cb211
--- /dev/null
+++ b/debian/existDB.1
@@ -0,0 +1,51 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH EXISTDB "1" "May 2015" "existDB 0~20150520+2004" "User Commands"
+.SH NAME
+existDB \- manual page for existDB 0~20150520+2004
+.SH DESCRIPTION
+usage: existDB [stuff]
+.HP
+\fB\-mersize\fR mersize
+.HP
+\fB\-\-\fR Use the specified mersize when building existDB tables.
+.HP
+\fB\-build\fR some.fasta prefix
+.HP
+\fB\-\-\fR Build an existDB on all mers in some.fasta and save
+.IP
+the tables into prefix.
+.HP
+\fB\-describe\fR prefix
+.HP
+\fB\-\-\fR Reports the state of some existDB file.
+.HP
+\fB\-testfiles\fR some.fasta prefix
+.TP
+\fB\-\-\fR Build an existDB table from some.fasta.
+Write that table to disk.
+.TP
+Load the table back.
+Compare that each mer in some.fasta is present
+.IP
+in all three existDB tables created earlier.
+.HP
+\fB\-testexistence\fR some.fasta
+.HP
+\fB\-\-\fR Build an existDB table from some.fasta, check that every
+.TP
+mer in some.fasta can be found in the table.
+Does not
+.IP
+guarantee that every mer in the table is found in the file.
+.HP
+\fB\-testexhaustive\fR some.fasta some.meryl
+.HP
+\fB\-\-\fR Build an existDB table from some.fasta, check _EVERY_ mer
+.TP
+for existance.
+Complain if a mer exists in the table but
+.TP
+not in the meryl database.
+Assumes 'some.meryl' is the
+.IP
+mercount of some.fasta.
diff --git a/debian/kmer-mask.1 b/debian/kmer-mask.1
new file mode 100644
index 0000000..b9ae5b0
--- /dev/null
+++ b/debian/kmer-mask.1
@@ -0,0 +1,69 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH KMER-MASK "1" "May 2015" "kmer-mask 0~20150520+2004" "User Commands"
+.SH NAME
+kmer-mask \- manual page for kmer-mask 0~20150520+2004
+.SH DESCRIPTION
+usage: ./kmer\-mask [\-novel | \fB\-confirmed]\fR ...
+.TP
+\fB\-mdb\fR mer\-database
+load masking kmers from meryl 'mer\-database'
+.TP
+\fB\-ms\fR
+mer\-size
+.TP
+\fB\-edb\fR exist\-database
+save masking kmers to 'exist\-database' for faster restarts
+.TP
+\fB\-1\fR in.1.fastq
+input reads \- fastq, fastq.gz, fastq.bz2 or fastq.xz
+.HP
+\fB\-2\fR in.2.fastq \- (optional, but if not present,
messes up the output classification)
+.TP
+\fB\-o\fR
+out output reads:
+out.fullymasked.[12].fastq \- reads with below 'lowthreshold' bases
retained
+out.partiallymasked.[12].fastq \- reads in between
+out.retained.[12].fastq \- reads with more than 'hightreshold' bases
retained
+out.discarded.[12].fastq \- reads with conflicting status
+.TP
+\fB\-m\fR min\-size
+ignore database hits below this many consecutive kmers (0)
+.TP
+\fB\-e\fR extend\-size
+extend database hits across this many missing kmers (0)
+.TP
+\fB\-novel\fR
+RETAIN novel sequence not present in the database
+.TP
+\fB\-confirmed\fR
+RETAIN confirmed sequence present in the database
+.TP
+\fB\-promote\fR
+promote the lesser RETAINED read to the status of the more RETAINED read
+read1=fullymasked and read2=partiallymasked \-> both are partiallymasked
+.TP
+\fB\-demote\fR
+demote the more RETAINED read to the status of the lesser RETAINED read
+read1=fullymasked and read2=partiallymasked \-> both are fullymasked
+.TP
+\fB\-discard\fR
+discard pairs with conflicting status (DEFAULT)
+read1=fullymasked and read2=partiallymasked \-> both are discarded
+.SS "stats on stderr, number of sequences with amount RETAINED:"
+.TP
+\fB\-lowthreshold\fR t
+(0.3333)
+.TP
+\fB\-highthreshold\fR t
+(0.6667)
+.TP
+\fB\-h\fR histogram
+write a histogram of the amount of sequence RETAINED
+.TP
+\fB\-t\fR t
+use 't' compute threads
+.TP
+\fB\-v\fR
+show progress
+.PP
+ERROR: exactly one of \fB\-novel\fR and \fB\-confirmed\fR must be supplied.
diff --git a/debian/mapMers-depth.1 b/debian/mapMers-depth.1
new file mode 100644
index 0000000..8c2e73a
--- /dev/null
+++ b/debian/mapMers-depth.1
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH MAPMERS-DEPTH "1" "May 2015" "mapMers-depth 0~20150520+2004" "User
Commands"
+.SH NAME
+mapMers-depth \- manual page for mapMers-depth 0~20150520+2004
+.SH DESCRIPTION
+unknown option ''
+usage: ./mapMers\-depth \fB\-mers\fR MERYL \fB\-m\fR MERSIZE \fB\-seq\fR
IN.FASTA [\-count | \fB\-depth\fR | \fB\-stats]\fR > output
+.PP
+For sequence ordinal 's' and position in that sequence 'p':
+.HP
+\fB\-count\fR \- report the count (c) of the single kmer that starts at
position (p).
+.IP
+Format: 's p c'
+.TP
+\fB\-depth\fR \- report the number (n) of kmers that span position (p).
+Format: 's p n'
+.HP
+\fB\-stats\fR \- report the min (m), max (M), ave (a) count of all mers that
span
+.TP
+position (p).
+Format: 's p m M a t n'
+.IP
+(also reports total count (t) and number of kmers (n))
+.PP
+ERROR: No mer size (\fB\-m\fR) suppled.
+ERROR: No fasta input (\fB\-seq\fR) suppled.
+ERROR: No meryl database (\fB\-mers\fR) suppled.
+ERROR: Exactly one of \fB\-count\fR, \fB\-depth\fR and \fB\-stats\fR may be
supplied.
diff --git a/debian/mapMers.1 b/debian/mapMers.1
new file mode 100644
index 0000000..976229d
--- /dev/null
+++ b/debian/mapMers.1
@@ -0,0 +1,7 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH MAPMERS "1" "May 2015" "mapMers 0~20150520+2004" "User Commands"
+.SH NAME
+mapMers \- manual page for mapMers 0~20150520+2004
+.SH DESCRIPTION
+unknown option ''
+usage: ./mapMers [\-stats | \fB\-regions\fR | \fB\-details]\fR \fB\-m\fR
mersize \fB\-mers\fR mers \fB\-seq\fR fasta > output
diff --git a/debian/meryl.1 b/debian/meryl.1
new file mode 100644
index 0000000..f9e94af
--- /dev/null
+++ b/debian/meryl.1
@@ -0,0 +1,242 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH MERYL "1" "May 2015" "meryl 0~20150520+2004" "User Commands"
+.SH NAME
+meryl \- manual page for meryl 0~20150520+2004
+.SH DESCRIPTION
+usage: ./meryl [personality] [global options] [options]
+.SS "where personality is:"
+.HP
+\fB\-P\fR \fB\-\-\fR compute parameters
+.HP
+\fB\-B\fR \fB\-\-\fR build table
+.HP
+\fB\-S\fR \fB\-\-\fR scan table
+.HP
+\fB\-M\fR \fB\-\-\fR "math" operations
+.HP
+\fB\-D\fR \fB\-\-\fR dump table
+.PP
+\fB\-P\fR: Given a sequence file (\fB\-s\fR) or an upper limit on the
+.IP
+number of mers in the file (\fB\-n\fR), compute the table size
+(\fB\-t\fR in build) to minimize the memory usage.
+.TP
+\fB\-m\fR #
+(size of a mer; required)
+.TP
+\fB\-c\fR #
+(homopolymer compression; optional)
+.TP
+\fB\-p\fR
+(enable positions)
+.TP
+\fB\-s\fR seq.fasta
+(seq.fasta is scanned to determine the number of mers)
+.TP
+\fB\-n\fR #
+(compute params assuming file with this many mers in it)
+.TP
+Only one of \fB\-s\fR, \fB\-n\fR need to be specified.
+If both are given
+.HP
+\fB\-s\fR takes priority.
+.PP
+\fB\-B\fR: Given a sequence file (\fB\-s\fR) and lots of parameters, compute
+.TP
+the mer\-count tables.
+By default, both strands are processed.
+.TP
+\fB\-f\fR
+(only build for the forward strand)
+.TP
+\fB\-r\fR
+(only build for the reverse strand)
+.TP
+\fB\-C\fR
+(use canonical mers, assumes both strands)
+.TP
+\fB\-L\fR #
+(DON'T save mers that occur less than # times)
+.TP
+\fB\-U\fR #
+(DON'T save mers that occur more than # times)
+.TP
+\fB\-m\fR #
+(size of a mer; required)
+.TP
+\fB\-c\fR #
+(homopolymer compression; optional)
+.TP
+\fB\-p\fR
+(enable positions)
+.TP
+\fB\-s\fR seq.fasta
+(sequence to build the table for)
+.TP
+\fB\-o\fR tblprefix
+(output table prefix)
+.TP
+\fB\-v\fR
+(entertain the user)
+.IP
+By default, the computation is done as one large sequential process.
+Multi\-threaded operation is possible, at additional memory expense, as
+is segmented operation, at additional I/O expense.
+.IP
+Threaded operation: Split the counting in to n almost\-equally sized
+pieces. This uses an extra h MB (from \fB\-P\fR) per thread.
+.TP
+\fB\-threads\fR n
+(use n threads to build)
+.IP
+Segmented, sequential operation: Split the counting into pieces that
+will fit into no more than m MB of memory, or into n equal sized pieces.
+Each piece is computed sequentially, and the results are merged at the end.
+Only one of \fB\-memory\fR and \fB\-segments\fR is needed.
+.TP
+\fB\-memory\fR mMB
+(use at most m MB of memory per segment)
+.TP
+\fB\-segments\fR n
+(use n segments)
+.IP
+Segmented, batched operation: Same as sequential, except this allows
+each segment to be manually executed in parallel.
+Only one of \fB\-memory\fR and \fB\-segments\fR is needed.
+.TP
+\fB\-memory\fR mMB
+(use at most m MB of memory per segment)
+.TP
+\fB\-segments\fR n
+(use n segments)
+.TP
+\fB\-configbatch\fR
+(create the batches)
+.TP
+\fB\-countbatch\fR n
+(run batch number n)
+.TP
+\fB\-mergebatch\fR
+(merge the batches)
+.IP
+Initialize the compute with \fB\-configbatch\fR, which needs all the build
options.
+Execute all \fB\-countbatch\fR jobs, then \fB\-mergebatch\fR to complete.
+.IP
+meryl \fB\-configbatch\fR \fB\-B\fR [options] \fB\-o\fR file
+meryl \fB\-countbatch\fR 0 \fB\-o\fR file
+meryl \fB\-countbatch\fR 1 \fB\-o\fR file
+\&...
+meryl \fB\-countbatch\fR N \fB\-o\fR file
+meryl \fB\-mergebatch\fR N \fB\-o\fR file
+.IP
+Batched mode can run on the grid.
+.TP
+\fB\-sge\fR
+jobname unique job name for this execution. Meryl will submit
+jobs with name mpjobname, ncjobname, nmjobname, for
+phases prepare, count and merge.
+.TP
+\fB\-sgebuild\fR "options"
+any additional options to sge, e.g.,
+.TP
+\fB\-sgemerge\fR "options"
+"\-p \fB\-153\fR \fB\-pe\fR thread 2 \fB\-A\fR merylaccount"
+N.B. \- \fB\-N\fR will be ignored
+N.B. \- be sure to quote the options
+.PP
+\fB\-M\fR: Given a list of tables, perform a math, logical or threshold
operation.
+.IP
+Unless specified, all operations take any number of databases.
+.IP
+Math operations are:
+.TP
+min
+count is the minimum count for all databases. If the mer
+does NOT exist in all databases, the mer has a zero count, and
+is NOT in the output.
+.TP
+minexist
+count is the minimum count for all databases that contain the mer
+.TP
+max
+count is the maximum count for all databases
+.TP
+add
+count is sum of the counts for all databases
+.TP
+sub
+count is the first minus the second (binary only)
+.TP
+abs
+count is the absolute value of the first minus the second (binary only)
+.IP
+Logical operations are:
+.TP
+and
+outputs mer iff it exists in all databases
+.TP
+nand
+outputs mer iff it exists in at least one, but not all, databases
+.TP
+or
+outputs mer iff it exists in at least one database
+.TP
+xor
+outputs mer iff it exists in an odd number of databases
+.IP
+Threshold operations are:
+.TP
+lessthan x
+outputs mer iff it has count < x
+.TP
+lessthanorequal x
+outputs mer iff it has count <= x
+.TP
+greaterthan x
+outputs mer iff it has count > x
+.TP
+greaterthanorequal x
+outputs mer iff it has count >= x
+.TP
+equal x
+outputs mer iff it has count == x
+.IP
+Threshold operations work on exactly one database.
+.TP
+\fB\-s\fR tblprefix
+(use tblprefix as a database)
+.TP
+\fB\-o\fR tblprefix
+(create this output)
+.TP
+\fB\-v\fR
+(entertain the user)
+.TP
+NOTE:
+Multiple tables are specified with multiple \fB\-s\fR switches; e.g.:
+.IP
+\&./meryl \fB\-M\fR add \fB\-s\fR 1 \fB\-s\fR 2 \fB\-s\fR 3 \fB\-s\fR 4
\fB\-o\fR all
+.TP
+NOTE:
+It is NOT possible to specify more than one operation:
+.IP
+\&./meryl \fB\-M\fR add \fB\-s\fR 1 \fB\-s\fR 2 \fB\-sub\fR \fB\-s\fR 3
+.IP
+will NOT work.
+.PP
+\fB\-D\fR: Dump the table (not all of these work).
+.TP
+\fB\-Dd\fR
+Dump a histogram of the distance between the same mers.
+.TP
+\fB\-Dt\fR
+Dump mers >= a threshold. Use \fB\-n\fR to specify the threshold.
+.TP
+\fB\-Dc\fR
+Count the number of mers, distinct mers and unique mers.
+.TP
+\fB\-Dh\fR
+Dump (to stdout) a histogram of mer counts.
+.TP
+\fB\-s\fR
+Read the count table from here (leave off the .mcdat or .mcidx).
diff --git a/debian/positionDB.1 b/debian/positionDB.1
new file mode 100644
index 0000000..ce397f3
--- /dev/null
+++ b/debian/positionDB.1
@@ -0,0 +1,67 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
+.TH POSITIONDB "1" "May 2015" "positionDB 0~20150520+2004" "User Commands"
+.SH NAME
+positionDB \- manual page for positionDB 0~20150520+2004
+.SH DESCRIPTION
+usage: ./positionDB [args]
+.TP
+\fB\-mersize\fR k
+The size of the mers, default=20.
+.TP
+\fB\-merskip\fR k
+The skip between mers, default=0
+.TP
+\fB\-use\fR a\-b,c
+Specify which sequences to use, default=all
+.TP
+\fB\-merbegin\fR b
+Build on a subset of the mers, starting at mer #b, default=all mers
+.TP
+\fB\-merend\fR e
+Build on a subset of the mers, ending at mer #e, default=all mers
+.TP
+\fB\-sequence\fR s.fasta
+Input sequences.
+.TP
+\fB\-output\fR p.posDB
+Output filename.
+.IP
+To dump information about an image:
+.HP
+\fB\-dump\fR datafile
+.IP
+To run sanity tests:
+.HP
+\fB\-buildonly\fR [build opts] sequence.fasta
+.TP
+\fB\-\-\fR
+just builds a table and exits
+.HP
+\fB\-existence\fR [build opts] sequence.fasta
+.TP
+\fB\-\-\fR
+builds (or reads) a table reports if any mers
+in sequence.fasta cannot be found
+.HP
+\fB\-extra\fR [build opts] sequence.fasta
+.TP
+\fB\-\-\fR
+builds (or reads) a table reports if any mers
+NOT in sequence.fasta are be found
+.HP
+\fB\-test1\fR sequence.fasta
+.TP
+\fB\-\-\fR
+Tests if each and every mer is found in the
+positionDB. Reports if it doesn't find a mer
+at the correct position. Doesn't report if table
+has too much stuff.
+.HP
+\fB\-test2\fR db.fasta sequence.fasta
+.TP
+\fB\-\-\fR
+Builds a positionDB from db.fasta, then searches
+the table for each mer in sequence.fasta. Reports
+all mers it finds.
+.IP
+\fB\-\-\fR This is a silly test and you shouldn't do it.
--
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