Changeset 3698


Ignore:
Timestamp:
Sep 25, 2017, 6:37:50 AM (5 years ago)
Author:
Peter
Message:

merge release 0.14.4 into trunk

Location:
trunk
Files:
10 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/NEWS

    r3688 r3698  
    1414
    1515yat 0.14.x series from http://dev.thep.lu.se/yat/svn/branches/0.14-stable
     16
     17version 0.14.4 (released 25 September 2017)
     18  - BamWriteIterator default constructor is now implemented (bug #894)
     19  - Fixed bug that InBamFile::n_mapped(tid) and
     20    InBamFile::n_unmapped(tid) threw when tid contained no reads (#895)
     21  - utility::basename("") now returns "." (bug #893)
     22
     23  A complete list of closed tickets can be found here [[br]]
     24  http://dev.thep.lu.se/yat/query?status=closed&milestone=yat+0.14.4
    1625
    1726version 0.14.3 (released 22 March 2017)
  • trunk/m4/version.m4

    r3636 r3698  
    8585# yat-0.14.2 11:2:0
    8686# yat-0.14.3 11:3:0
     87# yat-0.14.4 11:4:0
    8788#
    8889# *Accidently, the libtool number was not updated for yat 0.5
  • trunk/test/bam.cc

    r3682 r3698  
    395395                << in.n_no_coordinate() << " expected: 0\n";
    396396  }
     397  // test that idxstats works also when tid is empty (no reads, bug #895)
     398  try {
     399    if (in.n_mapped(0)!=0) {
     400      suite.add(false);
     401      suite.err() << "error: InBamFile::n_mapped: "
     402                  << in.n_mapped(0) << " expected: 0\n";
     403    }
     404    if (in.n_unmapped(0)!=0) {
     405      suite.add(false);
     406      suite.err() << "error: InBamFile::n_unmapped: "
     407                  << in.n_unmapped(0) << " expected: 0\n";
     408    }
     409  }
     410  catch (utility::runtime_error& e) {
     411    suite.add(false);
     412    suite.err() << "error: exception: " << e.what() << "\n";
     413  }
    397414
    398415  BamRead bam;
  • trunk/test/bam_iterator.cc

    r3210 r3698  
    11// $Id$
    22//
    3 // Copyright (C) 2012, 2013, 2014 Peter Johansson
     3// Copyright (C) 2012, 2013, 2014, 2017 Peter Johansson
    44//
    55// This program is free software; you can redistribute it and/or modify
     
    110110  std::string outname("bam_iterator.bam");
    111111  OutBamFile out(outname, in.header());
     112  BamWriteIterator default_constructed;
     113  test::avoid_compiler_warning(default_constructed);
    112114  BamWriteIterator bam_out(out);
    113115  std::copy(BamReadIterator(in), BamReadIterator(), bam_out);
  • trunk/test/utility.cc

    r3661 r3698  
    688688  path.push_back(".");
    689689  path.push_back("..");
     690  path.push_back("");
    690691  std::vector<std::string> dir;
    691692  dir.push_back("/usr");
     
    693694  dir.push_back(".");
    694695  dir.push_back("/");
     696  dir.push_back(".");
    695697  dir.push_back(".");
    696698  dir.push_back(".");
     
    718720  path.push_back(".");
    719721  path.push_back("..");
     722  path.push_back("");
    720723  std::vector<std::string> file;
    721724  file.push_back("lib");
     
    725728  file.push_back(".");
    726729  file.push_back("..");
     730  file.push_back(".");
    727731  assert(file.size()==path.size());
    728732  using utility::basename;
  • trunk/yat/omic/BamFile.cc

    r3693 r3698  
    126126    uint64_t unmapped;
    127127#if YAT_HAVE_HTSLIB
    128     if (hts_idx_get_stat(index(), tid, &mapped, &unmapped)) {
     128    if (tid >= header().n_targets())
    129129      throw utility::runtime_error("InBamFile::get_idx_stat");
    130     }
     130    hts_idx_get_stat(index(), tid, &mapped, &unmapped);
    131131#else
    132132    index(); // ensure index_ is loaded
  • trunk/yat/omic/BamWriteIterator.cc

    r3114 r3698  
    33
    44/*
    5   Copyright (C) 2012, 2013 Peter Johansson
     5  Copyright (C) 2012, 2013, 2017 Peter Johansson
    66
    77  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    5353
    5454
     55  BamWriteIterator::BamWriteIterator(void)
     56  {}
     57
     58
    5559  BamWriteIterator::BamWriteIterator(OutBamFile& out)
    5660    : boost::function_output_iterator<BamWriter>(BamWriter(out))
  • trunk/yat/omic/BamWriteIterator.h

    r3147 r3698  
    55
    66/*
    7   Copyright (C) 2012, 2013 Peter Johansson
     7  Copyright (C) 2012, 2013, 2017 Peter Johansson
    88
    99  This file is part of the yat library, http://dev.thep.lu.se/yat
     
    9292
    9393       result is not dereferencable
     94
     95       \since Function was not implemented prior 0.14.4
    9496     */
    9597    BamWriteIterator(void);
  • trunk/yat/utility/utility.cc

    r3682 r3698  
    4343  std::string basename(const std::string& path)
    4444  {
     45    if (path.empty())
     46      return ".";
    4547    if (path.size()==1)
    4648      return path;
     
    98100  std::string dirname(const std::string& path)
    99101  {
    100     if (path.size()==1) {
     102    if (path.size()<=1) {
    101103      if (path=="/")
    102104        return path;
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