-------------------------------------------------------------
+--------------------------------------------------------------------------------
README : BAMTOOLS
-------------------------------------------------------------
+--------------------------------------------------------------------------------
-BamTools: a C++ API for reading/writing BAM files.
+BamTools: a C++ API & toolkit for reading/writing/manipulating BAM files.
I. Introduction
-II. Usage
-III. Contact
+ a. The API
+ b. The Toolkit
-------------------------------------------------------------
+II. Installation
+III. Usage
+ a. The API
+ b. The Toolkit
+
+IV. License
+
+V. Acknowledgements
+
+VI. Contact
+
+--------------------------------------------------------------------------------
I. Introduction:
+--------------------------------------------------------------------------------
+
+BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files.
+
+----------------------------------------
+Ia. The API:
+----------------------------------------
+
+The API consists of 2 main modules: BamReader and BamWriter. As you would
+expect, BamReader provides read-access to BAM files, while BamWriter handles
+writing data to BAM files. BamReader provides the interface for random-access
+(jumping) in a BAM file, as well as generating BAM index files.
+
+BamMultiReader is an extra module that allows you to manage multiple open BAM
+files for reading. It provides some validation & bookkeeping under the hood to
+keep all files sync'ed up for you.
+
+Additional files used by the API:
+
+ - BamAlignment.* : implements the BamAlignment data structure
+
+ - BamAux.h : contains various constants, data structures and utility
+ methods used throught the API.
+
+ - BamIndex.* : implements both the standard BAM format index (".bai") as
+ well as a new BamTools-specific index (".bti").
+
+ - BGZF.* : contains our implementation of the Broad Institute's BGZF
+ compression format.
+
+----------------------------------------
+Ib. The Toolkit:
+----------------------------------------
+
+If you've been using the BamTools since the early days, you'll notice that our
+'toy' API examples (BamConversion, BamDump, BamTrim,...) are now gone. We have
+dumped these in favor of a suite of small utilities that we hope both
+developers and end-users find useful:
+
+usage: bamtools [--help] COMMAND [ARGS]
+
+Available bamtools commands:
+
+ convert Converts between BAM and a number of other formats
+ count Prints number of alignments in BAM file(s)
+ coverage Prints coverage statistics from the input BAM file
+ filter Filters BAM file(s) by user-specified criteria
+ header Prints BAM header information
+ index Generates index for BAM file
+ merge Merge multiple BAM files into single file
+ random Select random alignments from existing BAM file(s)
+ sort Sorts the BAM file according to some criteria
+ split Splits a BAM file on user-specifed property, creating a
+ new BAM output file for each value found
+ stats Prints some basic statistics from input BAM file(s)
+
+See 'bamtools help COMMAND' for more information on a specific command.
+
+--------------------------------------------------------------------------------
+II. Installation :
+--------------------------------------------------------------------------------
+
+----------------------------------------
+IIa. Get CMake
+----------------------------------------
+
+BamTools has been migrated to a CMake-based build system. We believe that this
+should simplify the build process across all platforms, especially as the
+BamTools API moves into a shared library (that you link to instead of compiling
+lots of source files directly into your application). CMake is available on all
+major platforms, and indeed comes *out-of-the-box* with many Linux distributions.
+
+To see if you have CMake (and which version), try this command:
+
+ $ cmake --version
+
+BamTools requires CMake version >= 2.6.4. If you are missing CMake or have an
+older version, check your OS package manager (for Linux) or download it here:
+http://www.cmake.org/cmake/resources/software.html .
-The API consists of 2 main modules - BamReader and BamWriter. As you would expect,
-BamReader provides read-access to BAM files, while BamWriter does the writing of BAM
-files. BamReader provides an interface for random-access (jumping) in a BAM file,
-as well as generating BAM index files.
+----------------------------------------
+IIb. Build BamTools
+----------------------------------------
+
+Ok, now that you have CMake ready to go, let's build BamTools. A good
+practice in building applications is to do an out-of-source build, meaning
+that we're going to set up an isolated place to hold all the intermediate
+installation steps.
+
+In the top-level directory of BamTools, type the following commands:
+
+ $ mkdir build
+ $ cd build
+ $ cmake ..
+
+Windows users:
+This creates a Visual Studio solution file, which can then be built to create
+the toolkit executable and API DLL's.
+
+Everybody else:
+After running cmake, just run:
+
+ $ make
+
+Then go back up to the BamTools root directory.
+
+ $ cd ..
+
+----------------------------------------
+IIIb. Check It
+----------------------------------------
+
+Assuming the build process finished correctly, you should be able to find the
+toolkit executable here:
+
+ ./bin/
+
+The BamTools-associated libraries will be found here:
+
+ ./lib/
+
+The BamTools API headers will be found here:
-An additional file, BamAux.h, is included as well.
-This file contains the common data structures and typedefs used throught the API.
+ ./include/*
+
+--------------------------------------------------------------------------------
+III. Usage :
+--------------------------------------------------------------------------------
+
+** General usage information - perhaps explain common terms, point to SAM/BAM
+spec, etc **
+
+----------------------------------------
+IIIa. The API
+----------------------------------------
+
+The API, as noted above, contains 2 main modules - BamReader & BamWriter - for
+dealing with BAM files. Alignment data is made available through the
+BamAlignment data structure.
+
+A simple (read-only) scenario for accessing BAM data would look like the
+following:
+
+ // open our BamReader
+ BamReader reader;
+ reader.Open("someData.bam", "someData.bam.bai");
+
+ // define our region of interest
+ // in this example: bases 0-500 on the reference "chrX"
+ int id = reader.GetReferenceID("chrX");
+ BamRegion region(id, 0, id, 500);
+ reader.SetRegion(region);
+
+ // iterate through alignments in this region,
+ // ignoring alignments with a MQ below some cutoff
+ BamAlignment al;
+ while ( reader.GetNextAlignment(al) ) {
+ if ( al.MapQuality >= 50 )
+ // do something
+ }
+
+ // close the reader
+ reader.Close();
+
+To use this API in your application, you simply need to do the following:
+
+ 1 - Build the BamTools library (see Installation steps above).
+
+ 2 - Import BamTools API functionality as needed, for example:
+
+ #include "api/BamReader.h"
+ #include "api/BamWriter.h"
+ using namespace BamTools; // all BamTools classes/methods live within
+ // this namespace
+
+ 3 - In your own build step, point your include path to the
+ (BAMTOOLS_ROOT)/include directory. Link your app with '-lbamtools' ('l'
+ as in Lima).
+
+* You may need to modify the -L flag (library path) as well to help your linker
+find the (BAMTOOLS_ROOT)/lib directory.
+
+* Depending on your platform and where you install the BamTools API library, you
+may also need to adjust how your app locates the library at runtime. For
+Windows users, this can be as simple as dropping the DLL in the same folder as
+your executable. For *nix users (using gcc at least), you can add the following
+to your app's CXXFLAGS:
+
+ -Wl,-rpath,$(BAMTOOLS_LIB_DIR)
+
+where BAMTOOLS_LIB_DIR is, as you would guess, the directory containing the libs.
+An alternative is to set your local LD_LIBRARY_PATH environment variable.
+
+See any included programs for more detailed usage examples. See comments in the
+header files for more detailed API documentation.
+
+Note - For users that don't want to bother with the new BamTools shared library
+scheme: you are certainly free to just compile the API source code directly into
+your application, but be aware that the files involved are subject to change.
+Meaning that filenames, number of files, etc. are not fixed. You will also need
+to be sure to link with '-lz' for ZLIB functionality (linking with '-lbamtools'
+gives you this automatically).
+
+----------------------------------------
+IIIb. The Toolkit
+----------------------------------------
+
+BamTools provides a small, but powerful suite of command-line utility programs
+for manipulating and querying BAM files for data.
+
+--------------------
+Input/Output
+--------------------
+
+All BamTools utilities handle I/O operations using a common set of arguments.
+These include:
+
+ -in <BAM file>
+
+The input BAM files(s).
+
+ If a tool accepts multiple BAM files as input, each file gets its own "-in"
+ option on the command line. If no "-in" is provided, the tool will attempt
+ to read BAM data from stdin.
+
+ To read a single BAM file, use a single "-in" option:
+ > bamtools *tool* -in myData1.bam ...ARGS...
+
+ To read multiple BAM files, use multiple "-in" options:
+ > bamtools *tool* -in myData1.bam -in myData2.bam ...ARGS...
+
+ To read from stdin (if supported), omit the "-in" option:
+ > bamtools *tool* ...ARGS...
+
+ -out <BAM file>
+
+The output BAM file.
+
+ If a tool outputs a result BAM file, specify the filename using this option.
+ If none is provided, the tool will typically write to stdout.
+
+ *Note: Not all tools output BAM data (e.g. count, header, etc.)
+
+ -region <REGION>
+
+A region of interest. See below for accepted 'REGION string' formats.
+
+ Many of the tools accept this option, which allows a user to only consider
+ alignments that overlap this region (whether counting, filtering, merging,
+ etc.).
+
+ An alignment is considered to overlap a region if any part of the alignments
+ intersects the left/right boundaries. Thus, a 50bp alignment at position 70
+ will overlap a region beginning at position 100.
+
+ REGION string format
+ ----------------------
+ A proper REGION string can be formatted like any of the following examples:
+ where 'chr1' is the name of a reference (not its ID)and '' is any valid
+ integer position within that reference.
+
+ To read
+ chr1 - only alignments on (entire) reference 'chr1'
+ chr1:500 - only alignments overlapping the region starting at
+ chr1:500 and continuing to the end of chr1
+ chr1:500..1000 - only alignments overlapping the region starting at
+ chr1:500 and continuing to chr1:1000
+ chr1:500..chr3:750 - only alignments overlapping the region starting at
+ chr1:500 and continuing to chr3:750. This 'spanning'
+ region assumes that the reference specified as the
+ right boundary will occur somewhere in the file after
+ the left boundary. On a sorted BAM, a REGION of
+ 'chr4:500..chr2:1500' will produce undefined
+ (incorrect) results. So don't do it. :)
+
+ *Note: Most of the tools that accept a REGION string will perform without an
+ index file, but typically at great cost to performance (having to
+ plow through the entire file until the region of interest is found).
+ For optimum speed, be sure that index files are available for your
+ data.
+
+ -forceCompression
+
+Force compression of BAM output.
+
+ When tools are piped together (see details below), the default behavior is
+ to turn off compression. This can greatly increase performance when the data
+ does not have to be constantly decompressed and recompressed. This is
+ ignored any time an output BAM file is specified using "-out".
+
+--------------------
+Piping
+--------------------
+
+Many of the tools in BamTools can be chained together by piping. Any tool that
+accepts stdin can be piped into, and any that can output stdout can be piped
+from. For example:
+
+> bamtools filter -in data1.bam -in data2.bam -mapQuality ">50" | bamtools count
+
+will give a count of all alignments in your 2 BAM files with a mapQuality of
+greater than 50. And of course, any tool writing to stdout can be piped into
+other utilities.
+
+--------------------
+The Tools
+--------------------
+
+ convert Converts between BAM and a number of other formats
+ count Prints number of alignments in BAM file(s)
+ coverage Prints coverage statistics from the input BAM file
+ filter Filters BAM file(s) by user-specified criteria
+ header Prints BAM header information
+ index Generates index for BAM file
+ merge Merge multiple BAM files into single file
+ random Select random alignments from existing BAM file(s)
+ sort Sorts the BAM file according to some criteria
+ split Splits a BAM file on user-specifed property, creating a new
+ BAM output file for each value found
+ stats Prints some basic statistics from input BAM file(s)
+
+----------
+convert
+----------
+
+Description: converts BAM to a number of other formats
+
+Usage: bamtools convert -format <FORMAT> [-in <filename> -in <filename> ...]
+ [-out <filename>] [other options]
+
+Input & Output:
+ -in <BAM filename> the input BAM file(s) [stdin]
+ -out <BAM filename> the output BAM file [stdout]
+ -format <FORMAT> the output file format - see below for
+ supported formats
+
+Filters:
+ -region <REGION> genomic region. Index file is recommended for
+ better performance, and is read
+ automatically if it exists. See 'bamtools
+ help index' for more details on creating
+ one.
+
+Pileup Options:
+ -fasta <FASTA filename> FASTA reference file
+ -mapqual print the mapping qualities
+
+SAM Options:
+ -noheader omit the SAM header from output
+
+Help:
+ --help, -h shows this help text
+
+** Notes **
+
+ - Currently supported output formats ( BAM -> X )
+
+ Format type FORMAT (command-line argument)
+ ------------ -------------------------------
+ BED bed
+ FASTA fasta
+ FASTQ fastq
+ JSON json
+ Pileup pileup
+ SAM sam
+ YAML yaml
+
+ Usage example:
+ > bamtools convert -format json -in myData.bam -out myData.json
+
+ - Pileup Options have no effect on formats other than "pileup"
+ SAM Options have no effect on formats other than "sam"
+
+----------
+count
+----------
+
+Description: prints number of alignments in BAM file(s).
+
+Usage: bamtools count [-in <filename> -in <filename> ...] [-region <REGION>]
+
+Input & Output:
+ -in <BAM filename> the input BAM file(s) [stdin]
+ -region <REGION> genomic region. Index file is recommended
+ for better performance, and is used
+ automatically if it exists. See
+ 'bamtools help index' for more details
+ on creating one
+
+Help:
+ --help, -h shows this help text
+
+----------
+coverage
+----------
+
+Description: prints coverage data for a single BAM file.
+
+Usage: bamtools coverage [-in <filename>] [-out <filename>]
+
+Input & Output:
+ -in <BAM filename> the input BAM file [stdin]
+ -out <filename> the output file [stdout]
+
+Help:
+ --help, -h shows this help text
+
+----------
+filter
+----------
+
+Description: filters BAM file(s).
+
+Usage: bamtools filter [-in <filename> -in <filename> ...]
+ [-out <filename> | [-forceCompression]]
+ [-region <REGION>]
+ [ [-script <filename] | [filterOptions] ]
+
+Input & Output:
+ -in <BAM filename> the input BAM file(s) [stdin]
+ -out <BAM filename> the output BAM file [stdout]
+ -region <REGION> only read data from this genomic region (see
+ README for more details)
+ -script <filename> the filter script file (see README for more
+ details)
+ -forceCompression if results are sent to stdout (like when
+ piping to another tool), default behavior
+ is to leave output uncompressed. Use this
+ flag to override and force compression
+
+General Filters:
+ -alignmentFlag <int> keep reads with this *exact* alignment flag
+ (for more detailed queries, see below)
+ -insertSize <int> keep reads with insert size that matches
+ pattern
+ -mapQuality <[0-255]> keep reads with map quality that matches
+ pattern
+ -name <string> keep reads with name that matches pattern
+ -queryBases <string> keep reads with motif that matches pattern
+ -tag <TAG:VALUE> keep reads with this key=>value pair
+
+Alignment Flag Filters:
+ -isDuplicate <true/false> keep only alignments that are marked as
+ duplicate [true]
+ -isFailedQC <true/false> keep only alignments that failed QC [true]
+ -isFirstMate <true/false> keep only alignments marked as first mate
+ [true]
+ -isMapped <true/false> keep only alignments that were mapped [true]
+ -isMateMapped <true/false> keep only alignments with mates that mapped
+ [true]
+ -isMateReverseStrand <true/false> keep only alignments with mate on reverse
+ strand [true]
+ -isPaired <true/false> keep only alignments that were sequenced as
+ paired [true]
+ -isPrimaryAlignment <true/false> keep only alignments marked as primary
+ [true]
+ -isProperPair <true/false> keep only alignments that passed paired-end
+ resolution [true]
+ -isReverseStrand <true/false> keep only alignments on reverse strand
+ [true]
+ -isSecondMate <true/false> keep only alignments marked as second mate
+ [true]
+
+Help:
+ --help, -h shows this help text
+
+ *****************
+ * Filter Script *
+ *****************
+
+The BamTools filter tool allows you to use an external filter script to define
+complex filtering behavior. This script uses what I'm calling properties,
+filters, and a rule - all implemented in a JSON syntax.
+
+ ** Properties **
+
+A 'property' is a typical JSON entry of the form:
+
+ "propertyName" : "value"
+
+Here are the property names that BamTools will recognize:
+
+ alignmentFlag
+ cigar
+ insertSize
+ isDuplicate
+ isFailedQC
+ isFirstMate
+ isMapped
+ isMateMapped
+ isMateReverseStrand
+ isPaired
+ isPrimaryAlignment
+ isProperPair
+ isReverseStrand
+ isSecondMate
+ mapQuality
+ matePosition
+ mateReference
+ name
+ position
+ queryBases
+ reference
+ tag
+
+For properties with boolean values, use the words "true" or "false".
+For example,
+
+ "isMapped" : "true"
+
+will keep only alignments that are flagged as 'mapped'.
+
+For properties with numeric values, use the desired number with optional
+comparison operators ( >, >=, <, <=, !). For example,
+
+ "mapQuality" : ">=75"
+
+will keep only alignments with mapQuality greater than or equal to 75.
+
+If you're familiar with JSON, you know that integers can be bare (without
+quotes). However, if you a comparison operator, be sure to enclose in quotes.
+
+For string-based properties, the above operators are available. In addition,
+ you can also use some basic pattern-matching operators. For example,
+
+ "reference" : "ALU*" // reference starts with 'ALU'
+ "name" : "*foo" // name ends with 'foo'
+ "cigar" : "*D*" // cigar contains a 'D' anywhere
+
+Notes -
+The reference property refers to the reference name, not the BAM reference
+numeric ID.
+
+The tag property has an extra layer, so that the syntax will look like this:
+
+ "tag" : "XX:value"
+
+where XX is the 2-letter SAM/BAM tag and value is, well, the value.
+Comparison operators can still apply to values, so tag properties of:
+
+ "tag" : "AS:>60"
+ "tag" : "RG:foo*"
+
+are perfectly valid.
+
+ ** Filters **
+
+A 'filter' is a JSON container of properties that will be AND-ed together. For
+example,
+
+{
+ "reference" : "chr1",
+ "mapQuality" : ">50",
+ "tag" : "NM:<4"
+}
+
+would result in an output BAM file containing only alignments from chr1 with a
+mapQuality >50 and edit distance of less than 4.
+
+A single, unnamed filter like this is the minimum necessary for a complete
+filter script. Save this file and use as the -script parameter and you should
+be all set.
+
+Moving on to more potent filtering...
+
+You can also define multiple filters.
+To do so, you just need to use the "filters" keyword along with JSON array
+syntax, like this:
+
+{
+ "filters" :
+ [
+ {
+ "reference" : "chr1",
+ "mapQuality" : ">50"
+ },
+ {
+ "reference" : "chr1",
+ "isReverseStrand" : "true"
+ }
+ ]
+}
+
+These filters will be (inclusive) OR-ed together by default. So you'd get a
+resulting BAM with only alignments from chr1 that had either mapQuality >50 or
+on the reverse strand (or both).
+
+ ** Rule **
+
+Alternatively to anonymous OR-ed filters, you can also provide what I've called
+a "rule". By giving each filter an "id", using this "rule" keyword you can
+describe boolean relationships between your filter sets.
+
+Available rule operators:
+
+ & // and
+ | // or
+ ! // not
+
+This might sound a little fuzzy at this point, so let's get back to an example:
+
+{
+ "filters" :
+ [
+ {
+ "id" : "filter1",
+ "reference" : "chr1",
+ "mapQuality" : ">50"
+ },
+ {
+ "id" : "filter2",
+ "reference" : "chr1",
+ "isReverseStrand" : "true"
+ },
+ {
+ "id" : "filter3",
+ "reference" : "chr1",
+ "queryBases" : "AGCT*"
+ }
+ ],
+
+ "rule" : " (filter1 | filter2) & !filter3 "
+}
+
+In this case, we would only retain aligments that passed filter 1 OR filter 2,
+AND also NOT filter 3.
+
+These are dummy examples, and don't make much sense as an actual query case. But
+hopefully this serves an adequate primer to get you started and discover the
+potential flexibility here.
+
+----------
+header
+----------
+
+Description: prints header from BAM file(s).
+
+Usage: bamtools header [-in <filename> -in <filename> ...]
+
+Input & Output:
+ -in <BAM filename> the input BAM file(s) [stdin]
+
+Help:
+ --help, -h shows this help text
+
+----------
+index
+----------
+
+Description: creates index for BAM file.
+
+Usage: bamtools index [-in <filename>] [-bti]
+
+Input & Output:
+ -in <BAM filename> the input BAM file [stdin]
+ -bti create (non-standard) BamTools index file
+ (*.bti). Default behavior is to create
+ standard BAM index (*.bai)
+
+Help:
+ --help, -h shows this help tex
+
+----------
+merge
+----------
+
+Description: merges multiple BAM files into one.
+
+Usage: bamtools merge [-in <filename> -in <filename> ...]
+ [-out <filename> | [-forceCompression]] [-region <REGION>]
+
+Input & Output:
+ -in <BAM filename> the input BAM file(s)
+ -out <BAM filename> the output BAM file
+ -forceCompression if results are sent to stdout (like when
+ piping to another tool), default behavior
+ is to leave output uncompressed. Use this
+ flag to override and force compression
+ -region <REGION> genomic region. See README for more details
+
+Help:
+ --help, -h shows this help text
+
+----------
+random
+----------
+
+Description: grab a random subset of alignments.
+
+Usage: bamtools random [-in <filename> -in <filename> ...]
+ [-out <filename>] [-forceCompression] [-n]
+ [-region <REGION>]
+
+Input & Output:
+ -in <BAM filename> the input BAM file [stdin]
+ -out <BAM filename> the output BAM file [stdout]
+ -forceCompression if results are sent to stdout (like when
+ piping to another tool), default behavior
+ is to leave output uncompressed. Use this
+ flag to override and force compression
+ -region <REGION> only pull random alignments from within this
+ genomic region. Index file is
+ recommended for better performance, and
+ is used automatically if it exists. See
+ 'bamtools help index' for more details
+ on creating one
+
+Settings:
+ -n <count> number of alignments to grab. Note that no
+ duplicate checking is performed [10000]
+
+Help:
+ --help, -h shows this help text
+
+----------
+sort
+----------
+
+Description: sorts a BAM file.
+
+Usage: bamtools sort [-in <filename>] [-out <filename>] [sortOptions]
+
+Input & Output:
+ -in <BAM filename> the input BAM file [stdin]
+ -out <BAM filename> the output BAM file [stdout]
+
+Sorting Methods:
+ -byname sort by alignment name
+
+Memory Settings:
+ -n <count> max number of alignments per tempfile
+ [10000]
+ -mem <Mb> max memory to use [1024]
+
+Help:
+ --help, -h shows this help text
+
+----------
+split
+----------
+
+Description: splits a BAM file on user-specified property, creating a new BAM
+output file for each value found.
+
+Usage: bamtools split [-in <filename>] [-stub <filename stub>]
+ < -mapped | -paired | -reference | -tag <TAG> >
+
+Input & Output:
+ -in <BAM filename> the input BAM file [stdin]
+ -stub <filename stub> prefix stub for output BAM files (default
+ behavior is to use input filename,
+ without .bam extension, as stub). If
+ input is stdin and no stub provided, a
+ timestamp is generated as the stub.
+
+Split Options:
+ -mapped split mapped/unmapped alignments
+ -paired split single-end/paired-end alignments
+ -reference split alignments by reference
+ -tag <tag name> splits alignments based on all values of TAG
+ encountered (i.e. -tag RG creates a BAM
+ file for each read group in original
+ BAM file)
+
+Help:
+ --help, -h shows this help text
+
+----------
+stats
+----------
+
+Description: prints general alignment statistics.
+
+Usage: bamtools stats [-in <filename> -in <filename> ...] [statsOptions]
+
+Input & Output:
+ -in <BAM filename> the input BAM file [stdin]
-BGZF.h & BGZF.cpp contain our implementation of the Broad Institute's
-BGZF compression format.
+Additional Stats:
+ -insert summarize insert size data
-BamConversion, BamDump, and BamTrim are 3 'toy' examples on how the API can be used.
+Help:
+ --help, -h shows this help text
-------------------------------------------------------------
+--------------------------------------------------------------------------------
+IV. License :
+--------------------------------------------------------------------------------
-II. Usage :
+Both the BamTools API and toolkit are released under the MIT License.
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth,
+ Michael Stromberg
-To use this API, you simply need to do 3 things:
+See included file LICENSE for details.
- 1 - Drop the BamTools files somewhere the compiler can find them.
- (i.e. in your source tree, or somewhere else in your include path)
+--------------------------------------------------------------------------------
+V. Acknowledgements :
+--------------------------------------------------------------------------------
- 2 - Import BamTools API with the following lines of code
- #include "BamReader.h" // as needed
- #include "BamWriter.h" // as needed
- using namespace BamTools;
-
- 3 - Compile with '-lz' ('l' as in Lima) to access ZLIB compression library
- (For VS users, I can provide you zlib headers - just contact me).
+ * Aaron Quinlan for several key feature ideas and bug fix contributions
+ * Baptiste Lepilleur for the public-domain JSON parser (JsonCPP)
+ * Heng Li, author of SAMtools - the original C-language BAM API/toolkit.
-See any included programs and Makefile for more specific compiling/usage examples.
-See comments in the header files for more detailed API documentation.
+--------------------------------------------------------------------------------
+VI. Contact :
+--------------------------------------------------------------------------------
-------------------------------------------------------------
+Feel free to contact me with any questions, comments, suggestions, bug reports,
+ etc.
-III. Contact :
+Derek Barnett
+Marth Lab
+Biology Dept., Boston College
-Feel free to contact me with any questions, comments, suggestions, bug reports, etc.
- - Derek Barnett
-
-http://sourceforge.net/projects/bamtools
+Email: barnetde@bc.edu
+Project Websites: http://github.com/pezmaster31/bamtools (ACTIVE SUPPORT)
+ http://sourceforge.net/projects/bamtools (major updates only)
projects / bamtools.git / blobdiff