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commit 7991619e43fde63616c9b3d274d70e2a96736434 Author: Afif Elghraoui <a...@debian.org> Date: Tue Oct 11 20:59:10 2016 -0700 Refer to upstream README for command reference I cannot continue maintaining the manpages without upstream support. Monitoring changes to the README and revising them for the manpages takes up too much time. --- debian/control | 1 - debian/man/HPCdaligner.1.md | 77 ------------------------------ debian/man/HPCmapper.1.md | 46 ------------------ debian/man/LAcat.1.md | 29 ----------- debian/man/LAcheck.1.md | 41 ---------------- debian/man/LAdump.1.md | 52 -------------------- debian/man/LAindex.1.md | 27 ----------- debian/man/LAmerge.1.md | 37 -------------- debian/man/LAshow.1.md | 72 ---------------------------- debian/man/LAsort.1.md | 31 ------------ debian/man/LAsplit.1.md | 33 ------------- debian/man/Makefile | 12 ----- debian/man/daligner.1 | 12 +++++ debian/man/daligner.1.md | 114 -------------------------------------------- debian/rules | 20 ++++---- 15 files changed, 24 insertions(+), 580 deletions(-) diff --git a/debian/control b/debian/control index 80804ba..fd26071 100644 --- a/debian/control +++ b/debian/control @@ -5,7 +5,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian. Uploaders: Afif Elghraoui <a...@ghraoui.name> Build-Depends: debhelper (>= 9), - pandoc, Standards-Version: 3.9.6 Homepage: https://dazzlerblog.wordpress.com Vcs-Git: git://anonscm.debian.org/debian-med/daligner.git diff --git a/debian/man/HPCdaligner.1.md b/debian/man/HPCdaligner.1.md deleted file mode 100644 index 48d2a66..0000000 --- a/debian/man/HPCdaligner.1.md +++ /dev/null @@ -1,77 +0,0 @@ -% HPCdaligner(1) 1.0 -% -% August 2015 - -# NAME - -HPCdaligner - generate a script to run **daligner**(1) - -# SYNOPSIS - -**HPCdaligner** [**-vbAI**] [**-k***int(14)*] [**-w***int(6)*] - [**-h***int(35)*] [**-t***int*] [**-M***int*] - [**-e***double(.70)*] [**-l***int(1000)*] [**-s***int(100)*] [**-H***int*] - [**-m***track*]+ [**-dal***int(4)*] [**-deg***int(25)*] - *path:db|dam* [*first:int*[-*last:int*]] - -# DESCRIPTION - -**HPCdaligner** writes a UNIX shell script to the standard output that consists -of a sequence of commands that effectively run **daligner**(1) on all pairs of -blocks of a split database and then externally sorts and merges them using -**LAsort**(1) and **LAmerge**(1) into a collection of alignment files with -names *path.#.las* where # ranges from 1 to the number of blocks the database -is split into. These sorted files if concatenated by say **LAcat**(1) -would contain all the alignments in sorted order (of a-read, then b-read, and so on). -Moreover, all overlaps for a given a-read are guaranteed to not be split across -files, so one can run artifact analyzers or error correction on each sorted -file in parallel. - -The database must have been previously split by **DBsplit**(1) and all the -parameters, except **-v**, **-dal**, and **-deg**, are passed through to the -calls to **daligner**(1). The defaults for these parameters are as for -**daligner**(1). The **-v** flag, for verbose-mode, is also passed to all -calls to **LAsort**(1) and **LAmerge**(1). **-dal** and **-deg** options are -described later. - -For a database divided into N sub-blocks, the calls to **daligner**(1) will -produce in total 2TN^2 .las files assuming daligner runs with T threads. -These will then be sorted and merged into N^2 sorted .las files, one for each -block pair. These are then merged in ceil(log_deg N) phases where the number of -files decreases geometrically in **-deg** until there is 1 file per row of the -N x N block matrix. So at the end one has N sorted .las files that when -concatenated would give a single large sorted overlap file. - -The **-dal** option (default 4) gives the desired number of block comparisons -per call to **daligner**(1). Some must contain *dal*-1 comparisons, and the -first *dal*-2 block comparisons even less, but the **HPCdaligner** "planner" -does the best it can to give an average load of dal block comparisons per -command. The **-deg** option (default 25) gives the maximum number of files -that will be merged in a single **LAmerge**(1) command. The planner makes the -most even k-ary tree of merges, where the number of levels is ceil(log_deg N). - -If the integers *first* and *last* are missing, then the script produced -is for every block in the database. If *first* is present, then -**HPCdaligner** produces an incremental script that compares blocks *first* -through *last* (*last* = *first* if not present) against each other and all -previous blocks 1 through *first*-1, and then incrementally updates the .las -files for blocks 1 through *first*-1, and creates the .las files for -blocks *first* through *last*. - -Each UNIX command line output by the **HPCdaligner** can be a batch job -(we use the && operator to combine several commands into one line to make this -so). Dependencies between jobs can be maintained simply by first running all -the **daligner**(1) jobs, then all the initial sort jobs, and then all the -jobs in each phase of the external merge sort. Each of these phases is -separated by an informative comment line for your scripting convenience. - -# SEE ALSO - -**daligner**(1) -**LAsort**(1) -**LAmerge**(1) -**LAshow**(1) -**LAcat**(1) -**LAsplit**(1) -**LAcheck**(1) -**HPCmapper**(1) diff --git a/debian/man/HPCmapper.1.md b/debian/man/HPCmapper.1.md deleted file mode 100644 index 7c8de5d..0000000 --- a/debian/man/HPCmapper.1.md +++ /dev/null @@ -1,46 +0,0 @@ -% HPCmapper(1) 1.0 -% -% August 2015 - -# NAME - -HPCmapper - generate a script to map reads - -# SYNOPSIS - -**HPCmapper** [**-vb**] [**-k***int(20)*] [**-w***int(6)*] [**-h***int(50)*] - [**-t***int*] [**-M***int*] [**-e***double(.85)*] - [**-l***int(1000)*] [**-s***int(100)*] [**-H***int*] - [**-m***track*]+ [**-dal***int(4)*] [**-deg***int(25)*] - *ref:db|dam* *reads:db|dam* [*first:int*[-*last:int*]] - -# DESCRIPTION - -**HPCmapper** writes a UNIX shell script to the standard output that -consists of a sequence of commands that effectively "maps" every read in -the DB *reads* against a reference set of sequences in the DB *ref*, -recording all the found local alignments in the sequence of files -*ref.reads.1.las*, *ref.reads.2.las*, and so on, where *ref.reads.k.las* -contains the alignments between all of *ref* and the k'th block of -*reads*. The parameters are exactly the same as for **HPCdaligner**(1) -save that the **-k**, **-h**, and **-e** defaults are set -appropriately for mapping, and the **-A** and **-I** options -make no sense as *ref* and *reads* are expected to be distinct -data sets. - -If the integers *first* and *last* are missing, then the -script produced is for every block in the database *reads*. -If *first* is present then **HPCmapper** produces an script -that compares blocks *first* through *last* (*last* = *first* -if not present) against DAM *ref*. - -# SEE ALSO - -**daligner**(1) -**LAsort**(1) -**LAmerge**(1) -**LAshow**(1) -**LAcat**(1) -**LAsplit**(1) -**LAcheck**(1) -**HPCdaligner**(1) diff --git a/debian/man/LAcat.1.md b/debian/man/LAcat.1.md deleted file mode 100644 index 8e1f472..0000000 --- a/debian/man/LAcat.1.md +++ /dev/null @@ -1,29 +0,0 @@ -% LAcat(1) 1.0 -% -% August 2015 - -# NAME - -LAcat - concatenate .las files - -# SYNOPSIS - -**LAcat** *source:las* > *target.las* - -# DESCRIPTION - -Given argument *source*, find all files *source*.1.las, *source*.2.las, ... -*source*.n.las where *source*.i.las exists for every i in [1,n]. Then -concatenate these files in order into a single .las file and pipe the result -to the standard output. - -# SEE ALSO - -**daligner**(1) -**LAsort**(1) -**LAmerge**(1) -**LAshow**(1) -**LAsplit**(1) -**LAcheck**(1) -**HPCdaligner**(1) -**HPCmapper**(1) diff --git a/debian/man/LAcheck.1.md b/debian/man/LAcheck.1.md deleted file mode 100644 index 6525fa7..0000000 --- a/debian/man/LAcheck.1.md +++ /dev/null @@ -1,41 +0,0 @@ -% LAcheck(1) 1.0 -% -% August 2015 - -# NAME - -LAcheck - verify structural integrity of .las files - -# SYNOPSIS - -**LAcheck** [**-vS**] *src1:db|dam* [*src2:db|dam*] *align:las* ... - -# DESCRIPTION - -LAcheck checks each .las file for structural integrity, where the a- and -b-sequences come from *src1* or from *src1* and *src2*, respectively. -That is, it makes sure each file makes sense as a plausible .las file, -e.g. values are not out of bound, the number of records is correct, the number -of trace points for a record is correct, and so on. The exit status is 0 if -every file is deemed good, and 1 if at least one of the files looks corrupted. - -# OPTIONS - -**-S** -: Also check that the alignments are in sorted order - -**-v** -: Print a line for each .las file saying either the file is OK or reporting - the first error. If the **-v** option is not set, then the program - runs silently. - -# SEE ALSO - -**daligner**(1) -**LAsort**(1) -**LAmerge**(1) -**LAshow**(1) -**LAcat**(1) -**LAsplit**(1) -**HPCdaligner**(1) -**HPCmapper**(1) diff --git a/debian/man/LAdump.1.md b/debian/man/LAdump.1.md deleted file mode 100644 index 709f8d9..0000000 --- a/debian/man/LAdump.1.md +++ /dev/null @@ -1,52 +0,0 @@ -% LAdump(1) 1.0+20151214 -% -% January 2016 - -# NAME - -LAdump - display daligner local alignments in a simple format - -# SYNOPSIS - -**LAdump** [**-cdt**] [**-o**] *src1:db|dam* [ *src2:db|dam* ] - *align:las* [ *reads:FILE* | *reads:range* ... ] - -# DESCRIPTION - -Like **LAshow**(1), **LAdump** allows one to display the local alignments (LAs) of a subset of the -piles in an .las file and select which information to show about them. The difference -is that the information is written in a very simple "1-code" ASCII format that makes it -easy for one to read and parse the information for further use. For each LA the pair of -reads is output on a line. **-c** requests that one further output the coordinates of the -LA segments be output. The **-d** option requests that the number of difference in the LA -be output, and **-t** requests that the tracepoint information be output. Finally, **-o** -requests that only LAs that are proper overlaps be output. - -The format is very simple. Each requested piece of information occurs on a line. The -first character of every line is a "1-code" character that tells you what information -to expect on the line. The rest of the line contains information where each item is -separated by a single blank space. The trace point line gives the number of trace -point intervals in the LA and is immediately followed by that many lines containing -a pair of integers giving the # of differences and b-displacement in each successive -trace point interval. - - P #a #b - (#a,#b) have an LA between them - C #ab #ae #bb #be - [#ab,#ae] aligns with [#bb,#be] - D # - there are # differences in the LA - T #n - there are #n trace point intervals for the LA - (#d #y )^#n - there are #d difference aligning the #y bp's of B with the - next fixed-size interval of A - + X # - Total amount of X (X = P or T) - % X # - Maximum amount of X in any pile (X = P or T) - @ T # - Maximum number of trace points in any trace - -1-code lines that begin with +, %, or @ are always the first lines in the output. -They give size information about what is contained in the output. Specifically, -'+ X #' gives the total number of LAs (X=P), or the total number of trace point -intervals (X=T) in the file . '% X #' gives the maximum number of LAs (X=P) or -the maximum number of trace point intervals (X=T) in a given *pile* (collection of -LAs all with the same a-read (applies only to sorted .las files). Finally @ T # -gives the maximum # of trace point intervals in any trace within the file. - -# SEE ALSO -**daligner**(1) diff --git a/debian/man/LAindex.1.md b/debian/man/LAindex.1.md deleted file mode 100644 index b583a0d..0000000 --- a/debian/man/LAindex.1.md +++ /dev/null @@ -1,27 +0,0 @@ -% LAindex(1) 1.0+20151214 -% -% January 2016 - -# NAME - -LAindex - index Daligner alignment files - -# SYNOPSIS - -**LAindex** **-v** *source:las* ... - -# DESCRIPTION - -**LAindex** takes a series of one or more sorted .las files and produces a "pile -index" for each one. If the input file has name *X.las*, then the name of its -index file is *.X.las.idx*. For each A-read pile encoded in the .las file, -the index contains the offset to the first local alignment with A in the file. -The index starts with four 64-bit integers that encode the numbers % P, + T, % T, -and @ T described for **LAdump**(1), and then an offset for each pile beginning -with the first A-read in the file (which may not be read 0). The index is meant -to allow programs that process piles to more efficiently read just the piles -they need at any momment int time, as opposed to having to sequentially scan -through the .las file. - -# SEE ALSO -**daligner**(1) diff --git a/debian/man/LAmerge.1.md b/debian/man/LAmerge.1.md deleted file mode 100644 index 7a38d4b..0000000 --- a/debian/man/LAmerge.1.md +++ /dev/null @@ -1,37 +0,0 @@ -% LAmerge(1) 1.0 -% -% August 2015 - -# NAME - -LAmerge - merge .las files into a single sorted file - -# SYNOPSIS - -**LAmerge** [**-v**] *merge:las* *parts:las* `...` - -# DESCRIPTION - -Merge the .las files *parts* into a singled sorted file *merge*, where it is -assumed that the input *parts* files are sorted. Due to operating system -limits, the number of *parts* files must be <= 252. With the **-v** option -set, the program reports the number of records read and written. - -Used correctly, **LAmerge** and **LAsort**(1) together allow one to perform -an "external" sort that produces a collection of sorted files containing in -aggregate all the local alignments found by the **daligner**(1), such that -their concatenation is sorted in order of (a,b,o,ab). In particular, this -means that all the alignments for a given a-read will be found consecutively -in one of the files. So computations that need to look at all the alignments -for a given read can operate in simple sequential scans of these sorted files. - -# SEE ALSO - -**daligner**(1) -**LAsort**(1) -**LAshow**(1) -**LAcat**(1) -**LAsplit**(1) -**LAcheck**(1) -**HPCdaligner**(1) -**HPCmapper**(1) diff --git a/debian/man/LAshow.1.md b/debian/man/LAshow.1.md deleted file mode 100644 index f9c0c21..0000000 --- a/debian/man/LAshow.1.md +++ /dev/null @@ -1,72 +0,0 @@ -% LAshow(1) 1.0 -% -% August 2015 - -# NAME - -LAshow - display local alignments from .las files - -# SYNOPSIS - -**LAshow** [**-caroUF**] [**-i***int(4)*] [**-w***int(100)*] -[**-b***int(10)*] *src1:db|dam* [*src2:db|dam*] *align:las* -[*reads:FILE* | *reads:range* ... ] - -# DESCRIPTION - -**LAshow** produces a printed listing of the local alignments contained in the -specified .las file, where the a- and b-reads come from *src1* or from *src1* -and *src2*, respectively. If a file or list of read ranges is given, then only -the overlaps for which the a-read is in the set specified by the file or list -are displayed. See **DBshow**(1) for an explanation of how the file and list -of read ranges are interpreted. - -# OPTIONS - -**-F** -: Reverse the roles of the a- and b- reads in the display - -**-U** -: Use uppercase for DNA sequence instead of the default lowercase - -**-i***indentation* -: Set the indent for the cartoon and/or alignment displays if they are - requested. (default: 4) - -**-b***num_symbols* -: Set the number of symbols on either side of the aligned segments in an - alignment display. (default: 10) - -**-w***w* -: This parameter is used for the display modes specified - by **-a** and **-r**. (default: 100) - -**-o** -: Only display alignments that are proper overlaps-- that is, where a - sequence end occurs at each end of the alignment - -## DISPLAY MODES - -**-c** -: Cartoon rendering of the alignment - -**-a**, **-r** -: Display an alignment of the local alignment - -The **-a** option puts exactly *w* columns per segment of -the display, whereas the **-r** option puts exactly *w* a-read symbols in each -segment of the display. The **-r** display mode is useful when one wants to -visually compare two alignments involving the same a-read. If a combination of -the **-c**, **-a**, and **-r** flags is set, then the cartoon comes first, -then the **-a** alignment, and lastly the **-r** alignment. - -# SEE ALSO - -**daligner**(1) -**LAsort**(1) -**LAmerge**(1) -**LAcat**(1) -**LAsplit**(1) -**LAcheck**(1) -**HPCdaligner**(1) -**HPCmapper**(1) diff --git a/debian/man/LAsort.1.md b/debian/man/LAsort.1.md deleted file mode 100644 index 2d8ee58..0000000 --- a/debian/man/LAsort.1.md +++ /dev/null @@ -1,31 +0,0 @@ -% LAsort(1) 1.0 -% -% August 2015 - -# NAME - -LAsort - sort .las alignment files - -# SYNOPSIS - -**LAsort** [**-v**] *align:las* ... - -# DESCRIPTION - -Sort each .las alignment file specified on the command line. For each file -it reads in all the overlaps in the file and sorts them in lexicographical -order of (a,b,o,ab) assuming each alignment is recorded as -a[ab,ae] x b^o[bb,be]. It then writes them all to a file named *align.S.las* -(assuming that the input file was *align.las*). With the **-v** option set, -the program reports the number of records read and written. - -## SEE ALSO - -**daligner**(1) -**LAmerge**(1) -**LAshow**(1) -**LAcat**(1) -**LAsplit**(1) -**LAcheck**(1) -**HPCdaligner**(1) -**HPCmapper**(1) diff --git a/debian/man/LAsplit.1.md b/debian/man/LAsplit.1.md deleted file mode 100644 index 3452d50..0000000 --- a/debian/man/LAsplit.1.md +++ /dev/null @@ -1,33 +0,0 @@ -% LAsplit(1) 1.0 -% -% August 2015 - -# NAME - -LAsplit - divide an .las alignment file - -# SYNOPSIS - -**LAsplit** *target:las* {*parts:int* | *path:db|dam*} < *source.las* - -# DESCRIPTION - -If the second argument is an integer n, then divide the alignment file -*source*, piped in through the standard input, as evenly as possible into n -alignment files with the name *target.i.las* for i in [1,n], subject to the -restriction that all alignment records for a given a-read are in the same file. - -If the second argument refers to a database *path.db* that has been -partitioned, then divide the input alignment file into block .las files where -all records whose a-read is in *path.i.db* are in *align.i.las*. - -# SEE ALSO - -**daligner**(1) -**LAsort**(1) -**LAmerge**(1) -**LAshow**(1) -**LAcat**(1) -**LAcheck**(1) -**HPCdaligner**(1) -**HPCmapper**(1) diff --git a/debian/man/Makefile b/debian/man/Makefile deleted file mode 100644 index 7733e1b..0000000 --- a/debian/man/Makefile +++ /dev/null @@ -1,12 +0,0 @@ - -MANPAGES = $(basename $(wildcard *.1.md)) - -all: $(MANPAGES) - -%.1: %.1.md - pandoc -s -f markdown -t man $< > $@ - -clean: - $(RM) $(MANPAGES) - -.PHONY: clean diff --git a/debian/man/daligner.1 b/debian/man/daligner.1 new file mode 100644 index 0000000..2ab3eb8 --- /dev/null +++ b/debian/man/daligner.1 @@ -0,0 +1,12 @@ +.TH DALIGNER 1 "October 2016" +.SH NAME +daligner \- local alignment discovery between long nucleotide sequencing reads +.SH SYNOPSIS +.B daligner +.RI [ options ] " files" ... +.SH DESCRIPTION +These tools permit one to find all significant local alignments between reads encoded in a Dazzler database. +The assumption is that the reads are from a Pacific Biosciences RS II long read sequencer. +That is, the reads are long and noisy, up to 15% on average. +.SH OPTIONS +For a complete description of available commands and their options, see /usr/share/doc/daligner/README.md diff --git a/debian/man/daligner.1.md b/debian/man/daligner.1.md deleted file mode 100644 index acb4b22..0000000 --- a/debian/man/daligner.1.md +++ /dev/null @@ -1,114 +0,0 @@ -% DALIGNER(1) 1.0 -% -% August 2015 - -# NAME - -daligner - long read aligner - -# SYNOPSIS - -**daligner** -[**-vbAI**] -[**-k***int(14)*] [**-w***int(6)*] [**-h***int(35)*] -[**-t***int*] [**-M***int*] -[**-e***double(.70)*] [**-l***int(1000)*] [**-s***int(100)*] [**-H***int*] -[**-m***track*]+ *subject:db|dam* *target:db|dam* ... - -# DESCRIPTION -Compare sequences in the trimmed *subject* block against those in the list of -*target* blocks searching for local alignments involving at least **-l** base -pairs (default 1000) or more, that have an average correlation rate of **-e** -(default 70%). The local alignments found will be output in a sparse encoding -where a trace point on the alignment is recorded every **-s** base pairs of -the a-read (default 100bp). Reads are compared in both orientations and local -alignments meeting the criteria are output to one of several created files -described below. The **-v** option turns on a verbose reporting mode that gives -statistics on each major step of the computation. - -The options **-k**, **-h**, and **-w** control the initial filtration search -for possible matches between reads. Specifically, our search code looks for a -pair of diagonal bands of width 2^w (default 2^6 = 64) that contain a -collection of exact matching k-mers (default 14) between the two reads, -such that the total number of bases covered by the k-mer hits is h -(default 35). k cannot be larger than 32 in the current implementation. -If the **-b** option is set, then the **daligner** assumes the data has a -strong compositional bias (e.g. >65% AT rich), and at the cost of a bit more -time, dynamically adjusts k-mer sizes depending on compositional bias, so that -the mers used have an effective specificity of 4^k. - -If there are one or more interval tracks specified with the **-m** option, then -the reads of the DB or DB's to which the mask applies are soft masked with -the union of the intervals of all the interval tracks that apply, that is any -k-mers that contain any bases in any of the masked intervals are ignored for -the purposes of seeding a match. An interval track is a track, such as the -"dust" track created by DBdust, that encodes a set of intervals over either -the untrimmed or trimmed DB. - -Invariably, some k-mers are significantly over-represented (e.g. homopolymer -runs). These k-mers create an excessive number of matching k-mer pairs and -left unaddressed would cause daligner to overflow the available physical -memory. One way to deal with this is to explicitly set the **-t** parameter -which suppresses the use of any k-mer that occurs more than *t* times in either -the subject or target block. However, a better way to handle the situation is -to let the program automatically select a value of *t* that meets a given -memory usage limit specified (in Gb) by the **-M** parameter. By default -**daligner** will use the amount of physical memory as the choice for **-M**. -If you want to use less, say only 8Gb on a 24Gb HPC cluster node because you -want to run 3 **daligner** jobs on the node, then specify **-M***8*. -Specifying **-M***0* basically indicates that you do not want **daligner** to -self adjust k-mer suppression to fit within a given amount of memory. - -For each subject, target pair of blocks, say X and Y, the program reports -alignments where the a-read is in X and the b-read is in Y, and vice versa. -However, if the **-A** option is set ("A" for "asymmetric") then just overlaps -where the a-read is in X and the b-read is in Y are reported, and if X = Y, -then it further reports only those overlaps where the a-read index is less than the b-read index. In either case, if the **-I** option is set -("I" for "identity") then when X = Y, overlaps between different -portions of the same read will also be found and reported. - -Each found alignment is recorded as -- a[ab,ae] x bo[bb,be] -- where a and b -are the indices (in the trimmed DB) of the reads that overlap, o indicates -whether the b-read is from the same or opposite strand, and [ab,ae] and -[bb,be] are the intervals of a and bo, respectively, that align. The program -places these alignment records in files whose name is of the form -X.Y.[C|N]#.las where C indicates that the b-reads are complemented and N -indicates they are not (both comparisons are performed) and # is -the thread that detected and wrote out the collection of alignments contained -in the file. That is the file X.Y.O#.las contains the alignments produced by -thread # for which the a-read is from X and the b-read is from Y and in -orientation O. The command -**daligner -A** *X* *Y* produces 2\*NTHREAD thread files X.Y.?.las and -**daligner** *X* *Y* produces 4\*NTHREAD files X.Y.?.las and Y.X.?.las -(unless *X*=*Y* in which case only NTHREAD files, X.X.?.las, are produced). - -By default, **daligner** compares all overlaps between reads in the database -that are greater than the minimum cutoff set when the DB or DBs were split, -typically 1 or 2 Kbp. However, the HGAP assembly pipeline only wants to -correct large reads, say 8Kbp or over, and so needs only the overlaps where -the a-read is one of the large reads. By setting the **-H** parameter to say N, -one alters **daligner** so that it only reports overlaps where the a-read is -over N base-pairs long. - -While the default parameter settings are good for raw Pacbio data, **daligner** -can be used for efficiently finding alignments in corrected reads or other -less noisy reads. For example, for mapping applications against .dams, we run - -**daligner** **-k**20 **-h**60 **-e**.85 - -and on corrected reads, we typically run - -**daligner** **-k**25 **-w**5 **-h**60 **-e**.95 **-s**500 - -and at these settings it is very fast. - -# SEE ALSO - -**LAsort**(1) -**LAmerge**(1) -**LAshow**(1) -**LAcat**(1) -**LAsplit**(1) -**LAcheck**(1) -**HPCdaligner**(1) -**HPCmapper**(1) diff --git a/debian/rules b/debian/rules index dbae735..f66f8e7 100755 --- a/debian/rules +++ b/debian/rules @@ -1,7 +1,7 @@ #!/usr/bin/make -f #DH_VERBOSE = 1 -#include /usr/share/dpkg/default.mk +include /usr/share/dpkg/default.mk # The upstream build system doesn't honor CPPFLAGS CFLAGS := $(CPPFLAGS) $(CFLAGS) @@ -9,10 +9,14 @@ CFLAGS := $(CPPFLAGS) $(CFLAGS) %: dh $@ --parallel -override_dh_auto_build: - dh_auto_build - $(MAKE) -C debian/man - -override_dh_auto_clean: - dh_auto_clean - $(MAKE) -C debian/man clean +override_dh_auto_install: + dh_auto_install + mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1 + for command in $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/*; \ + do \ + if [ $$(basename $$command) != daligner ] ; \ + then \ + ln -s daligner.1 \ + $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/$$(basename $$command).1 ; \ + fi; \ + done -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/daligner.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit