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Viewing changes to ParseAligns/ParseAligns.cpp

  • Committer: Package Import Robot
  • Author(s): Shaun Jackman
  • Date: 2011-09-11 10:00:13 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: package-import@ubuntu.com-20110911100013-oa4m5fi036mjuwc8
Tags: 1.3.0-1
* New upstream release.
* Add libboost-graph-dev to Build-Depends.

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ParseAligns/ParseAligns.cpp
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#include "Estimate.h"
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#include "Histogram.h"
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#include "IOUtil.h"
 
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#include "MemoryUtil.h"
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#include "SAM.h"
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#include "StringUtil.h" // for toSI
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#include "Uncompress.h"
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#include <iterator>
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#include <sstream>
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#include <string>
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#include <unistd.h> // for sbrk
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#include <vector>
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using namespace std;
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"Report bugs to <" PACKAGE_BUGREPORT ">.\n";
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namespace opt {
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        static unsigned k;
 
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        unsigned k; // used by DistanceEst
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        static unsigned c;
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        static int verbose;
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        static string distPath;
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        static int inputFormat;
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        enum { KALIGNER, SAM };
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        int dot; // used by Estimate
 
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        /** Output format */
 
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        int format = ADJ; // used by Estimate
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}
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static const char shortopts[] = "d:k:f:h:c:v";
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        }
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}
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/** Start of the data segment. */
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static intptr_t sbrk0 = reinterpret_cast<intptr_t>(sbrk(0));
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static void printProgress(const ReadAlignMap& map)
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{
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        if (opt::verbose == 0)
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        size_t buckets = map.bucket_count();
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        if (stats.alignments % 1000000 == 0 || buckets != prevBuckets) {
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                ptrdiff_t bytes = reinterpret_cast<intptr_t>(sbrk(0)) - sbrk0;
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                prevBuckets = buckets;
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                size_t size = map.size();
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                cerr << "Read " << stats.alignments << " alignments. "
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                        "Hash load: " << size << " / " << buckets
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                        << " = " << (float)size / buckets
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                        << " using " << toSI(bytes) << "B." << endl;
 
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                        << " using " << toSI(getMemoryUsage()) << "B." << endl;
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        }
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}
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