Mostly cleaned up help & usage messages. Added MIT license.

diff --git a/LICENSE b/LICENSE
new file mode 100644 (file)
index 0000000..eaee1fd
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,22 @@
+The MIT License
+
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+

diff --git a/bamtools.cpp b/bamtools.cpp
index d80d96047e94917970cd586952bbfb780ed203b4..6a4343828aa14e8ac1ea7ae894d604550ab0b207 100644 (file)
--- a/bamtools.cpp
+++ b/bamtools.cpp
@@ -65,14 +65,14 @@ int Help(int argc, char* argv[]) {
     cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
     cerr << endl;
     cerr << "Available bamtools commands:" << endl;
-    cerr << "\tcoverage\tPrints coverage statistics from the input BAM file" << endl;
-    cerr << "\tdump\t\tDump BAM file contents to text output" << endl;                          // keep?
-    cerr << "\theader\t\tPrints BAM header information" << endl;
-    cerr << "\tindex\t\tGenerates index for BAM file" << endl;
-    cerr << "\tmerge\t\tMerge multiple BAM files into single file" << endl;
-    cerr << "\tsam\t\tPrints the BAM file in SAM (text) format" << endl;
-    cerr << "\tsort\t\tSorts the BAM file according to some criteria" << endl;
-    cerr << "\tstats\t\tPrints some basic statistics from the input BAM file" << endl;
+    cerr << "\tcoverage  Prints coverage statistics from the input BAM file" << endl;
+    cerr << "\tdump      Dump BAM file contents to text output" << endl;                          // keep?
+    cerr << "\theader    Prints BAM header information" << endl;
+    cerr << "\tindex     Generates index for BAM file" << endl;
+    cerr << "\tmerge     Merge multiple BAM files into single file" << endl;
+    cerr << "\tsam       Prints the BAM file in SAM (text) format" << endl;
+    cerr << "\tsort      Sorts the BAM file according to some criteria" << endl;
+    cerr << "\tstats     Prints some basic statistics from the input BAM file" << endl;
     cerr << endl;
     cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
     cerr << endl;

diff --git a/bamtools_coverage.h b/bamtools_coverage.h
index 083728aad1ecfa6083a0313536b060552da5b880..dcb8e23ccd4a89b4641f96e2bf74c12b3c1415b1 100644 (file)
--- a/bamtools_coverage.h
+++ b/bamtools_coverage.h
@@ -24,8 +24,9 @@ namespace BamTools {
 
 int BamCoverageHelp(void) { 
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools coverage [--in BAM file]" << std::endl;
-    std::cerr << "\t-i, --in\tInput BAM file to generate coverage stats\t[default=stdin]" << std::endl;
+    std::cerr << "usage:\tbamtools coverage [--in FILE]" << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t--in FILE  Input BAM file to generate coverage stats  [stdin]" << std::endl;
     std::cerr << std::endl;
     return 0;
 }
@@ -36,7 +37,7 @@ int RunBamCoverage(int argc, char* argv[]) {
     GetOpt options(argc, argv, 1);
     
     std::string inputFilename;
-    options.addOption('i', "in", &inputFilename);
+    options.addOption("in", &inputFilename);
     
     if ( !options.parse() ) return BamCoverageHelp();
     if ( inputFilename.empty() ) { inputFilename = "stdin"; }

diff --git a/bamtools_dump.h b/bamtools_dump.h
index 108caf22ef2234778383152e144276475e629a75..aac5ba18c6a7fccff4b0008576c8f157bbc735c8 100644 (file)
--- a/bamtools_dump.h
+++ b/bamtools_dump.h
@@ -27,8 +27,9 @@ namespace BamTools {
 
 int BamDumpHelp(void) { 
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools dump [BAM file1] [BAM file2] [BAM file3]..." << std::endl;
-    std::cerr << "\t[BAM file]\tInput file(s) to dump alignment summaries from [default=stdin]" << std::endl;
+    std::cerr << "usage:\tbamtools dump [--in FILE [FILE] [FILE] ...]" << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t--in FILE  Input file(s) to dump alignment summaries from  [stdin]" << std::endl;
     std::cerr << std::endl;
     return 0;
 }

diff --git a/bamtools_getopt.h b/bamtools_getopt.h
index 99ef6e2ff80a285f5803c816e0a87539e3e1d6d2..c3ff2d8cedaf6c75d3d3e0904bc3b0d4835a4d47 100644 (file)
--- a/bamtools_getopt.h
+++ b/bamtools_getopt.h
@@ -48,6 +48,7 @@ class GetOpt {
     public:
         // add standard option with arguments ( -Wall, -O2, --type=foo )
         void addOption(const char shortName, const std::string& longName, std::string* value);
+        void addOption(const std::string& longName, std::string* value);
         
         // add an option whose argument is optional (eg --log may default to dumping to stderr, unless a file is specified )
         // must provide a default string 
@@ -180,6 +181,12 @@ void GetOpt::addOption(const char shortName, const std::string& longName, std::s
     *value = std::string();
 }
 
+// add standard option with arguments ( -Wall, -O2, --type=foo )
+inline
+void GetOpt::addOption(const std::string& longName, std::string* value) {
+    addOption(0, longName, value);
+}
+
 // add an option whose argument is optional (eg --log may default to dumping to stderr, unless a file is specified )
 // must provide a default string 
 // short & long name version
@@ -548,4 +555,4 @@ void GetOpt::setSwitch(const Option& opt) {
 
 } // namespace BamTools 
 
-#endif // BAMTOOLS_GETOPT_H
\ No newline at end of file
+#endif // BAMTOOLS_GETOPT_H

diff --git a/bamtools_header.h b/bamtools_header.h
index f0544bb572df59a7a35b5290a5e94c13aa556616..ccace597f37765d5ec772a79ef145b9c91cd6215 100644 (file)
--- a/bamtools_header.h
+++ b/bamtools_header.h
@@ -25,8 +25,9 @@ namespace BamTools {
 
 int BamHeaderHelp(void) { 
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools header [BAM file1] [BAM file2] [BAM file3]..." << std::endl;
-    std::cerr << "\t[BAM file]\tInput file(s) to dump header contents from [default=stdin]" << std::endl;
+    std::cerr << "usage:\tbamtools header [--in FILE [FILE] [FILE] ...]" << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t--in FILE  Input file(s) to dump header contents from  [stdin]" << std::endl;
     std::cerr << std::endl;
     return 0;
 }

diff --git a/bamtools_index.h b/bamtools_index.h
index 1f9b4c8091af9ec7798fb24152d146215ddf8052..5c0a1b2e1915f080fda1edc39e8e8e2a3eee5e94 100644 (file)
--- a/bamtools_index.h
+++ b/bamtools_index.h
@@ -22,9 +22,10 @@ namespace BamTools {
 
 int BamIndexHelp(void) { 
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools index [--nclist] <BAM file>" << std::endl;
-    std::cerr << "\t--nclist\tUse NCList indexing scheme (faster?)\t[default=off] ** JUST HERE AS POSSIBLE SWITCH EXAMPLE FOR NOW **" << std::endl;
-    std::cerr << "\t<BAM file>\tInput BAM file to generate index from\t[req'd]" << std::endl;
+    std::cerr << "usage:\tbamtools index [--nclist] FILE" << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t--nclist  Use NCList indexing scheme (faster?)   [off] ** JUST HERE AS POSSIBLE SWITCH EXAMPLE FOR NOW **" << std::endl;
+    std::cerr << "\tFILE      Input BAM file to generate index from  [REQUIRED]" << std::endl;
     std::cerr << std::endl;
     return 0;
 }

diff --git a/bamtools_merge.h b/bamtools_merge.h
index 699f2d31ad3de02ac6374698beca22a7d38a8a6b..1f9be7086db690ac34eed1c5f727c118512d0642 100644 (file)
--- a/bamtools_merge.h
+++ b/bamtools_merge.h
@@ -27,9 +27,12 @@ namespace BamTools {
 
 int BamMergeHelp(void) { 
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools merge [--out FILE] --in <BAM file1> [BAM file2] [BAM file3]..." << std::endl;
-    std::cerr << "\t--in\tInput BAM file(s)\t\t[at least 1 req'd]" << std::endl;
-    std::cerr << "\t--out\tDestination for merge results\t[default=stdout]" << std::endl;
+    std::cerr << "usage:\tbamtools merge [--out FILE] [--region REGION] [--in FILE [FILE] [FILE] ...] " << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t--in FILE        Input BAM file(s)                      [stdin]" << std::endl;
+    std::cerr << "\t--region REGION  Only keep alignments from this region. [all alignments]" << std::endl;
+    std::cerr << "\t                 REGION format - (eg chr2:1000..2000)" << std::endl;
+    std::cerr << "\t--out FILE       Destination for merge results          [stdout]" << std::endl;
     std::cerr << std::endl;
     return 0;
 }
@@ -43,12 +46,16 @@ int RunBamMerge(int argc, char* argv[]) {
     GetOpt options(argc, argv, 1);
     
     std::string outputFilename = "";
-    options.addOption('o', "out", &outputFilename);
+    options.addOption("out", &outputFilename);
     
     std::vector<std::string> inputFilenames;
     options.addVariableLengthOption("in", &inputFilenames);
     
+    std::string regionString;
+    options.addOption("region", &regionString);
+    
     if ( !options.parse() || inputFilenames.empty() ) return BamMergeHelp();   
+    if ( inputFilenames.empty() ) { inputFilenames.push_back("stdin"); }
     if ( outputFilename.empty() ) { outputFilename = "stdout"; }
     
     // opens the BAM files without checking for indexes
@@ -63,12 +70,20 @@ int RunBamMerge(int argc, char* argv[]) {
     BamWriter writer;
     writer.Open(outputFilename, mergedHeader, references);
 
-    // store alignments to output file
-    BamAlignment bAlignment;
-    while (reader.GetNextAlignment(bAlignment)) {
-        writer.SaveAlignment(bAlignment);
+    // if desired region provided
+    if ( !regionString.empty() ) {
+        // parse region string
+        // only get alignments from this region
+    } 
+    
+    // else get all alignments
+    else {
+        // store alignments to output file
+        BamAlignment bAlignment;
+        while (reader.GetNextAlignment(bAlignment)) {
+            writer.SaveAlignment(bAlignment);
+        }
     }
-
     // clean & exit
     reader.Close();
     writer.Close();

diff --git a/bamtools_sam.h b/bamtools_sam.h
index 6bb38093f1ba49f7d8349ee29a9920f1fb812c31..b3fd0ef73ee5913b9a89e1536491ab65eb58a58a 100644 (file)
--- a/bamtools_sam.h
+++ b/bamtools_sam.h
@@ -27,13 +27,14 @@ int BamSamHelp(void) {
     // do we want to add a region specifier, eg 'chr2:1000..1500'? In this case, '--num' still makes sense (give me up to N alignments from this region)
   
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools sam [--in BAM file] [--num N] [--no_header]" << std::endl;
-    std::cerr << "\t-i, --in\tInput BAM file to generate SAM-format\t\t\t[default=stdin]" << std::endl;
-    std::cerr << "\t-n, --num N\tOnly print up to N alignments from beginning of file\t\t[default=50*]" << endl;  
-    std::cerr << "\t--no_header\tOmits SAM header information from output (alignments only)\t[default=off]" << std::endl;
+    std::cerr << "usage:\tbamtools sam [--in FILE] [--num N] [--no_header]" << std::endl;
     std::cerr << std::endl;
-    std::cerr << "* - By default bamtools sam will print all alignments in SAM format." << std::endl;
-    std::cerr << "    However if '-n' or '--num' is included with no N, the default of 50 is used." << std::endl;
+    std::cerr << "\t--in FILE    Input BAM file to generate SAM-format                       [stdin]" << std::endl;
+    std::cerr << "\t--num N      Only print up to N alignments from beginning of file        [50*]" << endl;  
+    std::cerr << "\t--no_header  Omits SAM header information from output (alignments only)  [off]" << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t* - By default bamtools sam will print all alignments in SAM format." << std::endl;
+    std::cerr << "\t    However if '--num' is included with no N, the default of 50 is used." << std::endl;
     std::cerr << std::endl;
     return 0;
 }
@@ -86,10 +87,10 @@ int RunBamSam(int argc, char* argv[]) {
     GetOpt options(argc, argv, 1);
     
     std::string inputFilename;
-    options.addOption('i', "in", &inputFilename);
+    options.addOption("in", &inputFilename);
     
     std::string numberString;
-    options.addOptionalOption('n', "num", &numberString, "50");
+    options.addOptionalOption("num", &numberString, "50");
     
     bool isOmittingHeader;
     options.addSwitch("no_header", &isOmittingHeader);
@@ -98,8 +99,8 @@ int RunBamSam(int argc, char* argv[]) {
     if ( inputFilename.empty() ) { inputFilename = "stdin"; }
     
     // maxNumberOfAlignments = all (if nothing specified)
-    //                       = 50  (if '-n' or '--num' but no N)
-    //                       = N   (if '-n N' or '--num N') 
+    //                       = 50  (if '--num' but no N)
+    //                       = N   (if '--num N') 
     int maxNumberOfAlignments = -1;
     if ( !numberString.empty() ) { maxNumberOfAlignments = atoi(numberString.c_str()); }
      

diff --git a/bamtools_sort.h b/bamtools_sort.h
index 18e435f9d03fc7a53ed4d54bbc4effa28fdc20de..e69a0b96830f54c909a845323c2c0c8aa354b928 100644 (file)
--- a/bamtools_sort.h
+++ b/bamtools_sort.h
@@ -21,9 +21,10 @@ namespace BamTools {
 
 int BamSortHelp(void) { 
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools sort [--in BAM file] [--out sorted BAM file]" << std::endl;
-    std::cerr << "\t-i, --in\tInput BAM file to sort\t[default=stdin]" << std::endl;
-    std::cerr << "\t-o. --out\tDestination of sorted BAM file\t[default=stdout]" << std::endl;
+    std::cerr << "usage:\tbamtools sort [--in FILE] [--out FILE]" << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t--in FILE   Input BAM file to sort          [stdin]" << std::endl;
+    std::cerr << "\t--out FILE  Destination of sorted BAM file  [stdout]" << std::endl;
     std::cerr << std::endl;
     return 0;
 }
@@ -34,10 +35,10 @@ int RunBamSort(int argc, char* argv[]) {
     GetOpt options(argc, argv, 1);
     
     std::string inputFilename;
-    options.addOption('i', "in", &inputFilename);
+    options.addOption("in", &inputFilename);
     
     std::string outputFilename;
-    options.addOption('o', "out", &outputFilename);
+    options.addOption("out", &outputFilename);
     
     if ( !options.parse() ) return BamCoverageHelp();
     if ( inputFilename.empty() )  { inputFilename  = "stdin"; }

diff --git a/bamtools_stats.h b/bamtools_stats.h
index fb991a265d1a9748e2b814901e220dd95eca0db7..4cbfedd3ea71b323cfbafd2ff82473db32db3337 100644 (file)
--- a/bamtools_stats.h
+++ b/bamtools_stats.h
@@ -24,8 +24,9 @@ namespace BamTools {
 
 int BamStatsHelp(void) { 
     std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools stats [--in BAM file]" << std::endl;
-    std::cerr << "\t-i, --in\tInput BAM file to calculate general stats\t[default=stdin]" << std::endl;
+    std::cerr << "usage:\tbamtools stats [--in FILE]" << std::endl;
+    std::cerr << std::endl;
+    std::cerr << "\t--in FILE  Input BAM file to calculate general stats  [stdin]" << std::endl;
     std::cerr << std::endl;
     return 0;
 }
@@ -36,7 +37,7 @@ int RunBamStats(int argc, char* argv[]) {
     GetOpt options(argc, argv, 1);
     
     std::string inputFilename;
-    options.addOption('t', "inp", &inputFilename);
+    options.addOption("in", &inputFilename);
     
     if ( !options.parse() ) return BamStatsHelp();
     if ( inputFilename.empty() ) { inputFilename = "stdin"; }