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bamtools print #185

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bamtools print #185

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45b4366
Added bamtools print capability for text summarization of aligned reg…
peskygobermouch Feb 24, 2019
c0214a5
added option for header line and extended revcomp beyond capital letters
peskygobermouch Mar 3, 2019
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1 change: 1 addition & 0 deletions src/toolkit/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ add_executable( bamtools_cmd
bamtools_header.cpp
bamtools_index.cpp
bamtools_merge.cpp
bamtools_print.cpp
bamtools_random.cpp
bamtools_resolve.cpp
bamtools_revert.cpp
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4 changes: 4 additions & 0 deletions src/toolkit/bamtools.cpp
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Expand Up @@ -19,6 +19,7 @@
#include "bamtools_header.h"
#include "bamtools_index.h"
#include "bamtools_merge.h"
#include "bamtools_print.h"
#include "bamtools_random.h"
#include "bamtools_resolve.h"
#include "bamtools_revert.h"
Expand All @@ -36,6 +37,7 @@ static const std::string FILTER = "filter";
static const std::string HEADER = "header";
static const std::string INDEX = "index";
static const std::string MERGE = "merge";
static const std::string PRINT = "print";
static const std::string RANDOM = "random";
static const std::string RESOLVE = "resolve";
static const std::string REVERT = "revert";
Expand Down Expand Up @@ -75,6 +77,7 @@ AbstractTool* CreateTool(const std::string& arg)
if (arg == HEADER) return new HeaderTool;
if (arg == INDEX) return new IndexTool;
if (arg == MERGE) return new MergeTool;
if (arg == PRINT) return new PrintTool;
if (arg == RANDOM) return new RandomTool;
if (arg == RESOLVE) return new ResolveTool;
if (arg == REVERT) return new RevertTool;
Expand Down Expand Up @@ -114,6 +117,7 @@ int Help(int argc, char* argv[])
std::cerr << "\theader Prints BAM header information" << std::endl;
std::cerr << "\tindex Generates index for BAM file" << std::endl;
std::cerr << "\tmerge Merge multiple BAM files into single file" << std::endl;
std::cerr << "\tprint Text printout of alignments at a location" << std::endl;
std::cerr << "\trandom Select random alignments from existing BAM file(s), intended "
"more as a testing tool."
<< std::endl;
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