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1 Beta Release 0.1.6 (2 September, 2009)
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2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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3
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4 Notable changes:
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5
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6 * In tview, do not show a blank screen when no reads mapped to the
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7 corresponding region.
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8
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9 * Implemented native HTTP support in the BGZF library. Samtools is now
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10 able to directly open a BAM file on HTTP. HTTP proxy is also
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11 supported via the "http_proxy" environmental variable.
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12
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13 * Samtools is now compitable with the MinGW (win32) compiler and the
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14 PDCurses library.
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15
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16 * The calmd (or fillmd) command now calculates the NM tag and replaces
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17 MD tags if they are wrong.
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18
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19 * The view command now recognizes and optionally prints FLAG in HEXs or
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20 strings to make a SAM file more friendly to human eyes. This is a
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21 samtools-C extension, not implemented in Picard for the time
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22 being. Please type `samtools view -?' for more information.
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23
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24 * BAM files now have an end-of-file (EOF) marker to facilitate
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25 truncation detection. A warning will be given if an on-disk BAM file
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26 does not have this marker. The warning will be seen on BAM files
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27 generated by an older version of samtools. It does NO harm.
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28
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29 * New key bindings in tview: `r' to show read names and `s' to show
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30 reference skip (N operation) as deletions.
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31
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32 * Fixed a bug in `samtools merge -n'.
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33
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34 * Samtools merge now optionally copies the header of a user specified
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35 SAM file to the resultant BAM output.
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36
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37 * Samtools pileup/tview works with a CIGAR with the first or the last
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38 operation is an indel.
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39
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40 * Fixed a bug in bam_aux_get().
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41
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42
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43 Changes in other utilies:
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44
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45 * Fixed wrong FLAG in maq2sam.
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46
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47
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48 (0.1.6: 2 September 2009, r453)
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49
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50
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51
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52 Beta Release 0.1.5 (7 July, 2009)
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53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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54
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55 Notable changes:
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56
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57 * Support opening a BAM alignment on FTP. Users can now use "tview" to
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58 view alignments at the NCBI ftp site. Please read manual for more
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59 information.
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60
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61 * In library, propagate errors rather than exit or complain assertion
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62 failure.
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63
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64 * Simplified the building system and fixed compiling errors caused by
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65 zlib<1.2.2.1.
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66
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67 * Fixed an issue about lost header information when a SAM is imported
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68 with "view -t".
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69
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70 * Implemented "samtool.pl varFilter" which filters both SNPs and short
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71 indels. This command replaces "indelFilter".
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72
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73 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
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74 pileup output.
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75
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76 * In pileup, cap mapping quality at 60. This helps filtering when
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77 different aligners are in use.
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78
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79 * In pileup, allow to output variant sites only.
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80
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81 * Made pileup generate correct calls in repetitive region. At the same
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82 time, I am considering to implement a simplified model in SOAPsnp,
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83 although this has not happened yet.
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84
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85 * In view, added '-u' option to output BAM without compression. This
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86 option is preferred when the output is piped to other commands.
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87
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88 * In view, added '-l' and '-r' to get the alignments for one library or
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89 read group. The "@RG" header lines are now partially parsed.
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90
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91 * Do not include command line utilities to libbam.a.
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92
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93 * Fixed memory leaks in pileup and bam_view1().
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94
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95 * Made faidx more tolerant to empty lines right before or after FASTA >
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96 lines.
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97
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98
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99 Changes in other utilities:
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100
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101 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.
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102
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103
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104 This release involves several modifications to the key code base which
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105 may potentially introduce new bugs even though we have tried to minimize
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106 this by testing on several examples. Please let us know if you catch
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107 bugs.
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108
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109 (0.1.5: 7 July 2009, r373)
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110
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111
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112
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113 Beta Release 0.1.4 (21 May, 2009)
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114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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115
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116 Notable changes:
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117
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118 * Added the 'rmdupse' command: removing duplicates for SE reads.
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119
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120 * Fixed a critical bug in the indel caller: clipped alignments are not
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121 processed correctly.
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122
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123 * Fixed a bug in the tview: gapped alignment may be incorrectly
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124 displayed.
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125
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126 * Unified the interface to BAM and SAM I/O. This is done by
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127 implementing a wrapper on top of the old APIs and therefore old APIs
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128 are still valid. The new I/O APIs also recognize the @SQ header
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129 lines.
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130
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131 * Generate the MD tag.
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132
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133 * Generate "=" bases. However, the indel caller will not work when "="
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134 bases are present.
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135
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136 * Enhanced support of color-read display (by Nils Homer).
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137
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138 * Implemented the GNU building system. However, currently the building
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139 system does not generate libbam.a. We will improve this later. For
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140 the time being, `make -f Makefile.generic' is preferred.
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141
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142 * Fixed a minor bug in pileup: the first read in a chromosome may be
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143 skipped.
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144
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145 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
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146 they were not used previously.
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147
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148 * Output the 'SM' tag from maq2sam.
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149
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150 (0.1.4: 21 May 2009, r297)
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151
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152
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153
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154 Beta Release 0.1.3 (15 April, 2009)
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155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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156
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157 Notable changes in SAMtools:
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158
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159 * SAMtools is more consistent with the specification: a) '*' in the
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160 QUAL field is allowed; b) the field separator is TAB only and SPACE
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161 is treated as a character in a field; c) empty header is allowed.
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162
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163 * Implemented GLFv3 support in pileup.
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164
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165 * Fixed a severe bug in fixmate: strand information is wrongly
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166 overwritten.
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167
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168 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
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169 not correctly retrieved sometimes.
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170
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171 * Fixed a bug in rmdup: segfault if unmapped reads are present.
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172
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173 * Move indel_filter.pl to samtools.pl and improved the filtering by
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174 checking the actual number of alignments containing indels. The indel
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175 pileup line is also changed a little to make this filtration easier.
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176
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177 * Fixed a minor bug in indexing: the bin number of an unmapped read is
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178 wrongly calculated.
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179
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180 * Added `flagstat' command to show statistics on the FLAG field.
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181
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182 * Improved indel caller by setting the maximum window size in local
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183 realignment.
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184
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185 Changes in other utilities:
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186
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187 * Fixed a bug in maq2sam: a tag name is obsolete.
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188
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189 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
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190 show the number of substitutions/indels/errors in read name; c)
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191 considerable code clean up.
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192
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193 * Various converters: improved functionality in general.
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194
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195 * Updated the example SAM due to the previous bug in fixmate.
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196
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197 (0.1.3: 15 April 2009, r227)
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198
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199
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200
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201 Beta Release 0.1.2 (28 January, 2008)
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202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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203
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204 Notable changes in SAMtools:
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205
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206 * Implemented a Bayesian indel caller. The new caller generate scores
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207 and genotype and is potentially more accurate than Maq's indel
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208 caller. The pileup format is also changed accordingly.
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209
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210 * Implemented rmdup command: remove potential PCR duplicates. Note that
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211 this command ONLY works for FR orientation and requires ISIZE is
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212 correctly set.
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213
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214 * Added fixmate command: fill in mate coordinates, ISIZE and mate
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215 related flags from a name-sorted alignment.
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216
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217 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.
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218
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219 * Allow to select reads shown in the pileup output with a mask.
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220
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221 * Generate GLFv2 from pileup.
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222
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223 * Added two more flags for flagging PCR/optical duplicates and for QC
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224 failure.
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225
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226 * Fixed a bug in sort command: name sorting for large alignment did not
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227 work.
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228
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229 * Allow to completely disable RAZF (using Makefile.lite) as some people
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230 have problem to compile it.
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231
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232 * Fixed a bug in import command when there are reads without
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233 coordinates.
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234
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235 * Fixed a bug in tview: clipping broke the alignment viewer.
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236
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237 * Fixed a compiling error when _NO_CURSES is applied.
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238
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239 * Fixed a bug in merge command.
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240
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241 Changes in other utilities:
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242
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243 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
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244 maq's reads simulator. Colin Hercus further improved it to allow
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245 longer indels.
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246
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247 * Added wgsim_eval.pl, a script that evaluates the accuracy of
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248 alignment on reads generated by wgsim.
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249
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250 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
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251 work properly when multiple hits are output.
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252
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253 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
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254 be retained when multiple hits are present.
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255
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256 * Fixed a bug in export2sam.pl for QC reads.
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257
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258 * Support RG tag at MAQ->SAM converter.
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259
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260 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
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261 indel are not properly handled, though.
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262
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263 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
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264 default Illumina output.
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265
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266 (0.1.2: 28 January 2008; r116)
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267
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268
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269
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270 Beta Release 0.1.1 (22 December, 2008)
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271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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272
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273 The is the first public release of samtools. For more information,
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274 please check the manual page `samtools.1' and the samtools website
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275 http://samtools.sourceforge.net |
