details: http://www.bx.psu.edu/hg/galaxy/rev/3ac95cd927d7 changeset: 3565:3ac95cd927d7 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Fri Mar 26 12:00:55 2010 -0400 description: Added new tabular/pileup join tool and associated test files. Also added pileup datatype. diffstat: datatypes_conf.xml.sample | 2 + lib/galaxy/datatypes/registry.py | 3 + lib/galaxy/datatypes/tabular.py | 93 ++ lib/galaxy/datatypes/test/10col.pileup | 30 + lib/galaxy/datatypes/test/6col.pileup | 30 + test-data/1.pileup | 1000 ++++++++++++++++++++++++++++++++ test-data/column_join_in1.pileup | 30 + test-data/column_join_in2.pileup | 30 + test-data/column_join_in3.pileup | 30 + test-data/column_join_in4.pileup | 25 + test-data/column_join_in5.pileup | 25 + test-data/column_join_in6.pileup | 25 + test-data/column_join_in7.pileup | 32 + test-data/column_join_in8.pileup | 23 + test-data/column_join_in9.pileup | 25 + test-data/column_join_out1.pileup | 60 + test-data/column_join_out2.pileup | 65 ++ test-data/column_join_out3.pileup | 70 ++ test/functional/test_get_data.py | 17 + tool_conf.xml.sample | 1 + 20 files changed, 1616 insertions(+), 0 deletions(-) diffs (1743 lines): diff -r 5f927f52191c -r 3ac95cd927d7 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Fri Mar 26 09:51:03 2010 -0400 +++ b/datatypes_conf.xml.sample Fri Mar 26 12:00:55 2010 -0400 @@ -61,6 +61,7 @@ <converter file="maf_to_interval_converter.xml" target_datatype="interval"/> </datatype> <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/> + <datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" /> <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/> <datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> <datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/> @@ -239,6 +240,7 @@ <sniffer type="galaxy.datatypes.interval:CustomTrack"/> <sniffer type="galaxy.datatypes.interval:Gff"/> <sniffer type="galaxy.datatypes.interval:Gff3"/> + <sniffer type="galaxy.datatypes.tabular:Pileup"/> <sniffer type="galaxy.datatypes.interval:Interval"/> <sniffer type="galaxy.datatypes.tabular:Sam"/> </sniffers> diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Fri Mar 26 09:51:03 2010 -0400 +++ b/lib/galaxy/datatypes/registry.py Fri Mar 26 12:00:55 2010 -0400 @@ -155,6 +155,7 @@ 'laj' : images.Laj(), 'lav' : sequence.Lav(), 'maf' : sequence.Maf(), + 'pileup' : tabular.Pileup(), 'qualsolid' : qualityscore.QualityScoreSOLiD(), 'qualsolexa' : qualityscore.QualityScoreSolexa(), 'qual454' : qualityscore.QualityScore454(), @@ -185,6 +186,7 @@ 'laj' : 'text/plain', 'lav' : 'text/plain', 'maf' : 'text/plain', + 'pileup' : 'text/plain', 'qualsolid' : 'text/plain', 'qualsolexa' : 'text/plain', 'qual454' : 'text/plain', @@ -218,6 +220,7 @@ interval.CustomTrack(), interval.Gff(), interval.Gff3(), + tabular.Pileup(), interval.Interval(), tabular.Sam() ] diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Fri Mar 26 09:51:03 2010 -0400 +++ b/lib/galaxy/datatypes/tabular.py Fri Mar 26 12:00:55 2010 -0400 @@ -327,3 +327,96 @@ except: pass return False + +class Pileup( Tabular ): + """Tab delimited data in pileup (6- or 10-column) format""" + file_ext = "pileup" + + """Add metadata elements""" + MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) + MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter ) + MetadataElement( name="baseCol", default=3, desc="Reference base column", param=metadata.ColumnParameter ) + + def init_meta( self, dataset, copy_from=None ): + Tabular.init_meta( self, dataset, copy_from=copy_from ) + + def set_peek( self, dataset, line_count=None, is_multi_byte=False ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + if line_count is None: + # See if line_count is stored in the metadata + if dataset.metadata.data_lines: + dataset.blurb = "%s genomic coordinates" % util.commaify( str( dataset.metadata.data_lines ) ) + else: + # Number of lines is not known ( this should not happen ), and auto-detect is + # needed to set metadata + dataset.blurb = "? genomic coordinates" + else: + dataset.blurb = "%s genomic coordinates" % util.commaify( str( line_count ) ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def make_html_table( self, dataset, skipchars=[] ): + """Create HTML table, used for displaying peek""" + out = ['<table cellspacing="0" cellpadding="3">'] + comments = [] + try: + # Generate column header + out.append('<tr>') + for i in range( 1, dataset.metadata.columns+1 ): + if i == dataset.metadata.chromCol: + out.append( '<th>%s.Chrom</th>' % i ) + elif i == dataset.metadata.startCol: + out.append( '<th>%s.Start</th>' % i ) + elif i == dataset.metadata.baseCol: + out.append( '<th>%s.Base</th>' % i ) + else: + out.append( '<th>%s</th>' % i ) + out.append('</tr>') + out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) + out.append( '</table>' ) + out = "".join( out ) + except Exception, exc: + out = "Can't create peek %s" % str( exc ) + return out + + def repair_methods( self, dataset ): + """Return options for removing errors along with a description""" + return [ ("lines", "Remove erroneous lines") ] + + def sniff( self, filename ): + """ + Checks for 'pileup-ness' + + There are two main types of pileup: 6-column and 10-column. For both, + the first three and last two columns are the same. We only check the + first three to allow for some personalization of the format. + + >>> fname = get_test_fname( 'interval.interval' ) + >>> Pileup().sniff( fname ) + False + >>> fname = get_test_fname( '6col.pileup' ) + >>> Pileup().sniff( fname ) + True + >>> fname = get_test_fname( '10col.pileup' ) + >>> Pileup().sniff( fname ) + True + """ + headers = get_headers( filename, '\t' ) + try: + for hdr in headers: + if hdr and not hdr[0].startswith( '#' ): + if len( hdr ) < 3: + return False + try: + # chrom start in column 1 (with 0-based columns) + # and reference base is in column 2 + check = int( hdr[1] ) + assert hdr[2] in [ 'A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n' ] + except: + return False + return True + except: + return False diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/test/10col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/10col.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,30 @@ +chrM 1 G G 25 0 25 1 ^:. I +chrM 2 T T 25 0 25 1 . I +chrM 3 T T 25 0 25 1 . I +chrM 4 A A 36 0 25 3 .^:.^:. II+ +chrM 5 A A 36 0 25 3 ... III +chrM 6 T T 36 0 25 3 ... III +chrM 7 G G 42 0 25 5 ...^:.^:. IIIII +chrM 8 T T 45 0 25 6 .....^:. IIIIII +chrM 9 A A 51 0 25 8 ......^:.^:. IIIIIIII +chrM 10 G G 54 0 25 9 ........^:. IIIIIIIII +chrM 11 C C 57 0 25 10 .........^:. IIIIIIIIII +chrM 12 T T 60 0 25 11 ..........^:. IIIIIIIIIII +chrM 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIIIIIIIIIIIIIIII +chrM 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII +chrM 15 A A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII +chrM 16 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII +chrM 17 A A 87 0 25 20 .................... 9IIIIIIIIIIIIIIIIIII +chrM 18 A A 87 0 25 20 .................... @IIIIIIIIIIIIIIIIIII +chrM 19 T T 55 0 25 20 ..................GG IIIIIIIIIIIIIIIIII'A +chrM 20 A A 54 0 25 20 ..................C. IIIIIIIIIIIIIII2II#$ +chrM 21 T T 87 0 25 20 .................... IIIIIIIIIIIIIIIIIIII +chrM 22 A A 87 0 25 20 .................... IIIIIIIIIIIIIIAIIIII +chrM 23 A A 87 0 25 20 .................... 9IIIIIIIIII0IIIIIIII +chrM 24 A A 87 0 25 20 ........N........... IIIIIIII"IIIIICIIIII +chrM 25 G G 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII +chrM 26 C C 57 0 25 21 .......A............. IIHIDII&IIIIIIIIIIIII +chrM 27 A A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII +chrM 28 A A 99 0 25 24 ........................ 1FIIIIIIIIIIIIIIIIDEIIII +chrM 29 G G 55 0 25 24 ..................NN.... ;IIIIII+HII=IIIIII""IIII +chrM 30 G G 68 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII diff -r 5f927f52191c -r 3ac95cd927d7 lib/galaxy/datatypes/test/6col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/test/6col.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,30 @@ +chrM 42 C 1 ^:. I +chrM 43 C 2 .^:. II +chrM 44 T 2 .. II +chrM 45 A 3 ..^:. III +chrM 46 G 4 ...^:. IIII +chrM 47 A 5 ....^:, IIIII +chrM 48 T 5 ...., IIIII +chrM 49 G 5 ...., IIIII +chrM 50 A 5 ...., IIIII +chrM 51 G 5 ...., IIIII +chrM 52 T 5 ...., IIIII +chrM 53 A 5 ...., IIIII +chrM 54 T 5 ...., IIIII +chrM 55 T 5 ...., IIIII +chrM 56 C 5 ...., IIIII +chrM 57 T 5 ...., IIIII +chrM 58 T 5 ...., IIIII +chrM 59 A 5 ...., IIIII +chrM 60 C 5 ...., IIIII +chrM 61 T 5 ...., IIIII +chrM 62 C 5 ...., IIIII +chrM 63 C 5 ...., IIIII +chrM 64 A 5 ...., IIIII +chrM 65 T 5 ...., IIIII +chrM 66 A 5 ...., IIIII +chrM 67 A 5 ...., IIIII +chrM 68 A 5 ...., IIICI +chrM 69 C 5 ...., IIIII +chrM 70 A 5 ...., IIIII +chrM 71 C 5 ...., IIIII diff -r 5f927f52191c -r 3ac95cd927d7 test-data/1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,1000 @@ +chrM 42 C 1 ^:. I +chrM 43 C 2 .^:. II +chrM 44 T 2 .. II +chrM 45 A 3 ..^:. III +chrM 46 G 4 ...^:. IIII +chrM 47 A 5 ....^:, IIIII +chrM 48 T 5 ...., IIIII +chrM 49 G 5 ...., IIIII +chrM 50 A 5 ...., IIIII +chrM 51 G 5 ...., IIIII +chrM 52 T 5 ...., IIIII +chrM 53 A 5 ...., IIIII +chrM 54 T 5 ...., IIIII +chrM 55 T 5 ...., IIIII +chrM 56 C 5 ...., IIIII +chrM 57 T 5 ...., IIIII +chrM 58 T 5 ...., IIIII +chrM 59 A 5 ...., IIIII +chrM 60 C 5 ...., IIIII +chrM 61 T 5 ...., IIIII +chrM 62 C 5 ...., IIIII +chrM 63 C 5 ...., IIIII +chrM 64 A 5 ...., IIIII +chrM 65 T 5 ...., IIIII +chrM 66 A 5 ...., IIIII +chrM 67 A 5 ...., IIIII +chrM 68 A 5 ...., IIICI +chrM 69 C 5 ...., IIIII +chrM 70 A 5 ...., IIIII +chrM 71 C 5 ...., IIIII +chrM 72 A 5 ...., IAIII +chrM 73 T 5 ...., IIIII +chrM 74 A 5 ...., IIIII +chrM 75 G 5 ...., %IIII +chrM 76 G 5 T..., *IIII +chrM 77 C 5 .$..., GIIII +chrM 78 T 4 .$.., IIII +chrM 79 T 3 .., III +chrM 80 G 3 .$., I1I +chrM 81 G 2 .$, II +chrM 82 T 1 ,$ I +chrM 83 C 2 ^:.^:. II +chrM 84 C 2 .. II +chrM 85 T 2 .. II +chrM 86 A 2 .. II +chrM 87 G 2 .. II +chrM 88 C 2 .. II +chrM 89 C 2 .. II +chrM 90 T 2 .. II +chrM 91 T 2 .. II +chrM 92 T 2 .. II +chrM 93 T 2 .. II +chrM 94 T 2 .. II +chrM 95 A 2 .. II +chrM 96 T 2 .. II +chrM 97 T 2 .. II +chrM 98 A 2 .. II +chrM 99 G 2 .. II +chrM 100 T 2 .. II +chrM 101 T 2 .. II +chrM 102 A 2 .. II +chrM 103 T 2 .. II +chrM 104 T 2 .. II +chrM 105 A 2 .. IE +chrM 106 A 2 .. II +chrM 107 T 2 .. II +chrM 108 A 2 .. II +chrM 109 G 2 .. II +chrM 110 A 2 .. II +chrM 111 A 2 .. I2 +chrM 112 T 2 .. II +chrM 113 T 2 .. II +chrM 114 A 2 .. H7 +chrM 115 C 2 .. II +chrM 116 A 2 .. II +chrM 117 C 2 .. II +chrM 118 A 2 .$.$ F8 +chrM 156 T 1 ^:, & +chrM 157 C 1 , I +chrM 158 A 2 g^:g I> +chrM 159 C 2 ,, /F +chrM 160 G 2 ,, II +chrM 161 T 2 ,, I> +chrM 162 C 2 ,, .- +chrM 163 T 2 ,, I8 +chrM 164 C 2 ,, 4F +chrM 165 T 2 ,, II +chrM 166 A 2 ,, II +chrM 167 C 2 ,, ;6 +chrM 168 G 2 ,, II +chrM 169 A 2 ,, II +chrM 170 T 2 ,, II +chrM 171 T 2 ,, IB +chrM 172 A 2 ,, II +chrM 173 A 2 ,, II +chrM 174 A 2 ,, II +chrM 175 A 2 ,, II +chrM 176 G 2 ,, II +chrM 177 G 2 ,, II +chrM 178 A 2 ,, II +chrM 179 G 2 ,, II +chrM 180 C 2 ,, II +chrM 181 A 3 ,,^:, III +chrM 182 G 3 ,,, III +chrM 183 G 3 ,,, III +chrM 184 T 3 ,,, III +chrM 185 A 3 ,,, III +chrM 186 T 3 ,,, III +chrM 187 C 3 ,,, III +chrM 188 A 3 ,,, III +chrM 189 A 3 ,,, III +chrM 190 G 3 ,,, III +chrM 191 C 3 ,$,, III +chrM 192 A 2 ,, II +chrM 193 C 2 ,$, II +chrM 194 A 1 , I +chrM 195 C 1 , I +chrM 196 T 1 , F +chrM 197 A 1 , I +chrM 198 G 1 , I +chrM 199 A 1 , I +chrM 200 A 1 , I +chrM 201 A 2 ,^:. I- +chrM 202 G 2 ,. II +chrM 203 T 2 ,. II +chrM 204 A 2 ,. II +chrM 205 G 2 ,. I6 +chrM 206 C 2 ,. II +chrM 207 T 2 ,. I, +chrM 208 C 2 ,. II +chrM 209 A 2 ,. II +chrM 210 T 2 ,. II +chrM 211 A 2 ,. II +chrM 212 A 2 ,. IE +chrM 213 C 2 ,. IC +chrM 214 A 2 ,. I; +chrM 215 C 2 ,. II +chrM 216 C 2 ,$. II +chrM 217 T 1 . I +chrM 218 T 1 . I +chrM 219 G 1 T I +chrM 220 C 1 . I +chrM 221 T 1 . I +chrM 222 C 1 . E +chrM 223 A 1 . 4 +chrM 224 G 1 T 9 +chrM 225 C 1 . : +chrM 226 C 1 . ? +chrM 227 A 1 . . +chrM 228 C 1 . C +chrM 229 A 3 .^:,^:, %II +chrM 230 C 3 .,, 8II +chrM 231 C 3 .,, 9II +chrM 232 C 3 .,, III +chrM 233 C 3 .,, AI' +chrM 234 C 3 .,, DI+ +chrM 235 A 3 .,, &I@ +chrM 236 C 3 .$,a +I$ +chrM 237 G 2 ,, II +chrM 238 G 2 ,, II +chrM 239 G 2 ,, II +chrM 240 A 2 ,, II +chrM 241 C 2 ,, I+ +chrM 242 A 2 ,, II +chrM 243 C 2 ,, II +chrM 244 A 3 ,,^:, II; +chrM 245 G 3 ,,, II* +chrM 246 C 3 ,,n II" +chrM 247 A 3 ,,, III +chrM 248 G 4 ,,,^:. IIII +chrM 249 T 4 ,,,. II)I +chrM 250 G 4 ,,,. II2I +chrM 251 A 4 ,,,. II(I +chrM 252 T 4 ,,,. II*I +chrM 253 A 4 ,,,. II7I +chrM 254 A 4 ,,,. II1I +chrM 255 A 4 ,,,. II?I +chrM 256 A 4 ,,,. II9I +chrM 257 A 4 ,,,. II?I +chrM 258 T 4 ,,,. II$I +chrM 259 T 5 ,,,.^:. II&II +chrM 260 A 5 ,,,.. II,II +chrM 261 A 5 ,,,.. II/II +chrM 262 G 5 ,,,.. II5II +chrM 263 C 5 ,,a.. II%II +chrM 264 T 5 ,$,$,.. II%II +chrM 265 A 3 ,.. )II +chrM 266 T 3 ,.. +II +chrM 267 G 4 ,..^:. *III +chrM 268 A 4 ,... EIII +chrM 269 A 4 ,... =III +chrM 270 C 4 a... ;III +chrM 271 G 4 ,... ;III +chrM 272 A 4 ,... 8@II +chrM 273 A 4 ,... 1III +chrM 274 A 4 ,... ICII +chrM 275 G 4 ,... IIII +chrM 276 T 4 ,... IIII +chrM 277 T 4 ,... IIII +chrM 278 C 4 ,... IIII +chrM 279 G 4 ,$... IIII +chrM 280 A 3 ... III +chrM 281 C 3 ... GII +chrM 282 T 3 ... III +chrM 283 A 3 .$.. IFI +chrM 284 A 3 ..^:, IAI +chrM 285 G 3 .., ;II +chrM 286 T 4 ..,^:. IIII +chrM 287 C 4 ..,. II4I +chrM 288 A 4 ..,. @III +chrM 289 T 4 ..,. IIII +chrM 290 A 4 ..,. @:II +chrM 291 T 4 ..,. IIAI +chrM 292 T 4 ..,. IIII +chrM 293 A 4 ..,. 8;II +chrM 294 A 4 .$.,. I<II +chrM 295 A 3 .,. 4II +chrM 296 T 3 .,. III +chrM 297 A 3 .,. BII +chrM 298 A 3 .,. CII +chrM 299 G 3 .,. III +chrM 300 G 3 .,. ;II +chrM 301 G 3 .,. III +chrM 302 T 3 .$,. III +chrM 303 T 2 ,. II +chrM 304 G 2 ,. II +chrM 305 G 2 ,. II +chrM 306 T 2 ,. II +chrM 307 A 2 ,. II +chrM 308 A 2 ,. II +chrM 309 A 2 ,. II +chrM 310 T 2 ,. II +chrM 311 T 2 ,. II +chrM 312 T 3 ,.^:. III +chrM 313 C 3 ,.. III +chrM 314 G 3 ,.. III +chrM 315 T 3 ,.. III +chrM 316 G 3 ,.. III +chrM 317 C 3 ,.. III +chrM 318 C 3 ,.. III +chrM 319 A 3 ,$.. III +chrM 320 G 2 .. II +chrM 321 C 2 .$. II +chrM 322 C 1 . I +chrM 323 A 1 . I +chrM 324 C 1 . I +chrM 325 C 1 . I +chrM 326 G 1 . I +chrM 327 C 1 . I +chrM 328 G 1 . I +chrM 329 G 1 . I +chrM 330 T 1 . I +chrM 331 C 1 . I +chrM 332 A 1 . I +chrM 333 T 1 . I +chrM 334 A 1 . I +chrM 335 C 1 . I +chrM 336 G 1 . I +chrM 337 A 1 . I +chrM 338 T 1 . I +chrM 339 T 1 . I +chrM 340 A 1 . I +chrM 341 A 1 . D +chrM 342 C 1 . I +chrM 343 C 1 . I +chrM 344 C 1 . I +chrM 345 A 1 . I +chrM 346 A 1 . ; +chrM 347 A 1 .$ 7 +chrM 360 C 1 ^:. I +chrM 361 G 1 . I +chrM 362 G 1 . I +chrM 363 C 1 . I +chrM 364 G 1 . I +chrM 365 T 1 . I +chrM 366 A 1 . I +chrM 367 A 1 . I +chrM 368 A 1 . I +chrM 369 G 1 . I +chrM 370 C 1 . I +chrM 371 G 1 . I +chrM 372 T 1 . I +chrM 373 G 1 . I +chrM 374 T 1 . I +chrM 375 C 1 . I +chrM 376 A 1 . I +chrM 377 A 1 . I +chrM 378 A 1 . I +chrM 379 G 1 . I +chrM 380 A 1 . I +chrM 381 C 1 T I +chrM 382 T 1 . I +chrM 383 A 1 . I +chrM 384 A 1 . I +chrM 385 T 1 . I +chrM 386 A 1 G I +chrM 387 C 1 . I +chrM 388 C 1 . I +chrM 389 A 2 .^:. II +chrM 390 A 3 ..^:. III +chrM 391 A 3 ... >II +chrM 392 A 3 ... III +chrM 393 T 3 ... III +chrM 394 A 3 ... III +chrM 395 A 3 .$.. III +chrM 396 A 2 .. II +chrM 397 G 2 .. II +chrM 398 T 2 .. EI +chrM 399 T 2 .. II +chrM 400 A 3 ..^:. III +chrM 401 A 3 ... III +chrM 402 A 3 ... III +chrM 403 A 3 ... III +chrM 404 C 3 ... III +chrM 405 C 3 ... III +chrM 406 C 3 ... EII +chrM 407 A 3 ... III +chrM 408 G 3 ... III +chrM 409 T 3 ... 0II +chrM 410 T 3 ... III +chrM 411 A 4 ...^:, IIII +chrM 412 A 4 ..., FIII +chrM 413 G 4 ..., IIIH +chrM 414 C 4 ...a III2 +chrM 415 C 4 TTTt III7 +chrM 416 G 5 ...,^:, II?7: +chrM 417 T 5 ...,, ;IIE@ +chrM 418 A 5 ...,, IIIII +chrM 419 A 5 ...,, IIIII +chrM 420 A 5 ...,, FIIII +chrM 421 A 5 ...,, IIIII +chrM 422 A 5 ...,, >IIII +chrM 423 G 6 ...,,^:, HII/I, +chrM 424 C 6 .$..a,, ;II-I: +chrM 425 T 5 .$.,,, IIIIF +chrM 426 A 5 .,,,^:, III@I +chrM 427 C 5 .,,,, III$I +chrM 428 A 5 .,,,, IIIII +chrM 429 A 5 .,,,, IIII. +chrM 430 C 5 .,,,a I%I5' +chrM 431 C 5 .,,,, I(I5< +chrM 432 A 5 .,,,, IIIII +chrM 433 A 5 .,,,, 0IIII +chrM 434 A 5 .,,,, =IIII +chrM 435 G 5 .$,,,, EIIII +chrM 436 T 4 ,,,, III5 +chrM 437 A 4 ,,,, IIII +chrM 438 A 4 ,,,, IIII +chrM 439 A 4 ,,,, IIII +chrM 440 A 4 ,,,, IIIF +chrM 441 T 6 ,,,,^:.^:. III;II +chrM 442 A 6 ,,,,.. IIIIII +chrM 443 G 6 ,,,,.. IIIIII +chrM 444 A 6 ,,,,.. IIIIII +chrM 445 C 6 ,,,,.. IIIIII +chrM 446 T 6 ,$,,,.. IIIIII +chrM 447 A 5 ,,,.. IIIII +chrM 448 C 5 ,,,.. IIIII +chrM 449 G 6 ,,,..^:, IIIII6 +chrM 450 A 6 ,,,.., IIIIII +chrM 451 A 6 ,$,,.., IIIIII +chrM 452 A 5 ,,.., IIIII +chrM 453 G 5 ,,.., IIIII +chrM 454 T 6 ,,..,^:, IIIIII +chrM 455 G 6 ,,..,, IIIIII +chrM 456 A 6 ,,..,, IIIIII +chrM 457 C 6 ,,..,, IIIII= +chrM 458 T 6 ,$,..,, IIIIII +chrM 459 T 5 ,..,, IIIII +chrM 460 T 5 ,..,, IIIII +chrM 461 A 5 ,$..,, IIIII +chrM 462 A 4 ..,, IIII +chrM 463 T 4 ..,, IIIC +chrM 464 A 4 ..,, IIII +chrM 465 C 4 ..,, IIII +chrM 466 C 4 ..,, IIII +chrM 467 T 4 ..,, II>? +chrM 468 C 4 ..,, IIII +chrM 469 T 4 ..,, IIIG +chrM 470 G 4 ..,, %III +chrM 471 A 4 ..,, 4;II +chrM 472 C 4 ..,, II3I +chrM 473 T 4 ..,, IIII +chrM 474 A 4 ..,, ;III +chrM 475 C 4 ..,, IIII +chrM 476 A 4 .$.$,, 32II +chrM 477 C 2 ,, II +chrM 478 G 2 ,, II +chrM 479 A 2 ,, II +chrM 480 T 3 ,,^:. III +chrM 481 A 3 ,,. III +chrM 482 G 3 ,,. III +chrM 483 C 4 ,,.^:, IIIE +chrM 484 T 4 ,$,., III9 +chrM 485 A 3 ,., III +chrM 486 A 3 ,., III +chrM 487 G 3 ,., III +chrM 488 A 3 ,., III +chrM 489 C 3 ,$., III +chrM 490 C 2 ., II +chrM 491 C 2 ., II +chrM 492 A 2 ., II +chrM 493 A 2 ., II +chrM 494 A 2 ., II +chrM 495 C 2 ., II +chrM 496 T 2 ., I2 +chrM 497 G 2 ., II +chrM 498 G 2 ., II +chrM 499 G 2 ., II +chrM 500 A 2 ., II +chrM 501 T 2 ., II +chrM 502 T 2 ., II +chrM 503 A 2 ., II +chrM 504 G 2 ., II +chrM 505 A 2 ., GI +chrM 506 T 2 ., II +chrM 507 A 2 ., II +chrM 508 C 2 ., II +chrM 509 C 2 ., II +chrM 510 C 3 .,^:. III +chrM 511 C 3 .,. III +chrM 512 A 3 .,. 6II +chrM 513 C 3 .,. III +chrM 514 T 3 .,. III +chrM 515 A 3 .$,. III +chrM 516 T 2 ,. II +chrM 517 G 2 ,. II +chrM 518 C 3 ,$.^:. III +chrM 519 T 2 .. II +chrM 520 T 3 ..^:, III +chrM 521 A 3 .., III +chrM 522 G 3 .., II, +chrM 523 C 3 .., III +chrM 524 C 3 .., II7 +chrM 525 C 3 .., III +chrM 526 T 3 .., II? +chrM 527 A 3 .., III +chrM 528 A 3 .., III +chrM 529 A 3 .., FII +chrM 530 C 3 .., II+ +chrM 531 T 3 .., III +chrM 532 A 3 .., :II +chrM 533 A 3 .., DGI +chrM 534 A 3 .., III +chrM 535 A 3 .., ?CI +chrM 536 T 3 .., III +chrM 537 A 3 .., 9II +chrM 538 G 3 .., III +chrM 539 C 3 .., III +chrM 540 T 3 .., III +chrM 541 T 3 .., III +chrM 542 A 4 ..,^:. IIII +chrM 543 C 4 ..,. IIII +chrM 544 C 4 ..,. IIII +chrM 545 A 4 N$.,. "III +chrM 546 C 3 .,. III +chrM 547 A 3 .,. DII +chrM 548 A 3 .,. EII +chrM 549 C 3 .,. III +chrM 550 A 3 .,. III +chrM 551 A 3 .,. 6II +chrM 552 A 3 .,. GII +chrM 553 G 3 .$,. ?II +chrM 554 C 2 ,. I< +chrM 555 T 2 ,$. II +chrM 556 A 2 .^:. II +chrM 557 T 2 .. II +chrM 558 T 2 .. II +chrM 559 C 2 .. II +chrM 560 G 2 .. II +chrM 561 C 2 .. II +chrM 562 C 2 .. II +chrM 563 A 2 .. CI +chrM 564 G 2 .. II +chrM 565 A 2 .. GI +chrM 566 G 2 .. II +chrM 567 T 2 .. /I +chrM 568 A 2 .. DI +chrM 569 C 2 .. II +chrM 570 T 2 .. II +chrM 571 A 2 .. II +chrM 572 C 2 .. FI +chrM 573 T 2 .. 9I +chrM 574 A 2 .. II +chrM 575 G 2 .. II +chrM 576 C 2 .. II +chrM 577 A 3 .$.^:. III +chrM 578 A 2 .. II +chrM 579 C 2 .. II +chrM 580 A 3 ..^:, III +chrM 581 G 3 .., III +chrM 582 C 3 .., II? +chrM 583 C 3 ..a II- +chrM 584 T 3 .., IIH +chrM 585 A 3 .., III +chrM 586 A 3 .., III +chrM 587 A 4 ..,^:, IIII +chrM 588 A 4 ..,, IIII +chrM 589 C 4 ..,, IIII +chrM 590 T 4 ..,, II.5 +chrM 591 C 4 .$.,, II<I +chrM 592 A 3 .,, III +chrM 593 A 3 .,, III +chrM 594 A 3 .,, III +chrM 595 G 3 .,, III +chrM 596 G 3 .,, III +chrM 597 A 3 .,, :EI +chrM 598 C 3 .,, III +chrM 599 T 4 .,,^:. II@I +chrM 600 T 4 .,,. IIII +chrM 601 G 4 .,,. IIII +chrM 602 G 4 .,,. IIII +chrM 603 C 4 .,,. IIII +chrM 604 G 4 .,,. IIII +chrM 605 G 4 .,,. IIII +chrM 606 T 4 .,,. 5III +chrM 607 G 4 .,,. IIII +chrM 608 C 4 .,,. *III +chrM 609 T 5 .,,.^:, ?IIII +chrM 610 T 5 .,,., IIII8 +chrM 611 T 5 .,,., IIIII +chrM 612 A 5 T$,,., 3IIII +chrM 613 C 4 ,,., III) +chrM 614 A 4 ,,., IIII +chrM 615 T 4 ,$,., IIII +chrM 616 C 3 ,., III +chrM 617 C 3 ,., III +chrM 618 C 3 ,., III +chrM 619 T 3 ,., IF9 +chrM 620 C 3 ,., II7 +chrM 621 T 3 ,., III +chrM 622 A 3 ,$., I7I +chrM 623 G 2 ., II +chrM 624 A 2 ., 9I +chrM 625 G 2 ., II +chrM 626 G 2 ., II +chrM 627 A 2 ., 2I +chrM 628 G 2 ., II +chrM 629 C 2 ., II +chrM 630 C 2 ., II +chrM 631 T 2 ., II +chrM 632 G 2 ., II +chrM 633 T 2 ., II +chrM 634 T 2 .$, II +chrM 635 C 1 , I +chrM 636 C 1 , I +chrM 637 A 1 , I +chrM 638 T 1 , I +chrM 639 A 1 , I +chrM 640 A 1 , I +chrM 641 T 1 , I +chrM 642 C 1 , I +chrM 643 G 1 , I +chrM 644 A 1 ,$ I +chrM 646 A 1 ^:. I +chrM 647 A 1 . I +chrM 648 A 1 . I +chrM 649 C 2 .^:, II +chrM 650 C 2 ., II +chrM 651 C 2 ., II +chrM 652 C 3 .,^:, II) +chrM 653 G 3 .,, II2 +chrM 654 A 3 .,, III +chrM 655 T 4 .,,^:. II*I +chrM 656 A 4 .,,. IIII +chrM 657 A 4 .,,. IIII +chrM 658 A 4 .,,. IIII +chrM 659 C 4 .,,. IIII +chrM 660 C 4 .,,. IIII +chrM 661 C 4 .,,. IIII +chrM 662 C 4 .,,. IIFI +chrM 663 A 4 .,,. =IDI +chrM 664 C 4 .,,. II6I +chrM 665 C 5 .,,.^:, IIIII +chrM 666 A 5 .,,., BIIII +chrM 667 T 5 .,,., II5I+ +chrM 668 C 5 .,,., IIIII +chrM 669 C 5 .,,., IIIII +chrM 670 C 5 .,a., II.II +chrM 671 T 5 .,,., IIIIA +chrM 672 T 6 .,,.,^:. FI9I.I +chrM 673 G 6 .,,.,. IIIIII +chrM 674 C 6 .,,.,. IIIIII +chrM 675 T 6 .,,.,. IIIIII +chrM 676 A 6 .,,.,. ,IIEII +chrM 677 A 7 .,,.,.^:. 3II;III +chrM 678 T 7 .,,.,.. IIIIDII +chrM 679 T 7 .,,.,.. CIIIIII +chrM 680 C 7 .,,.,.. IIIIIII +chrM 681 A 7 .$,,.,.. 9IIIIII +chrM 682 G 6 ,,.,.. II$III +chrM 683 C 6 ,,.,.. IIIIII +chrM 684 C 6 ,$,.,.. IIIIII +chrM 685 T 5 ,.,.. IIIII +chrM 686 A 5 ,.,.. IIIII +chrM 687 T 5 ,$.,.. IIIII +chrM 688 A 4 .,.. IIII +chrM 689 T 4 .,.. IIII +chrM 690 A 4 .$,.. IIII +chrM 691 C 3 ,.. III +chrM 692 C 3 ,.. III +chrM 693 G 4 ,..^:, IIII +chrM 694 C 4 ,.., IIII +chrM 695 C 4 ,.., IIII +chrM 696 A 4 ,.., IIII +chrM 697 T 4 ,.., IIII +chrM 698 C 4 ,.., IIII +chrM 699 T 4 ,.., IIII +chrM 700 T 4 ,$.., IIII +chrM 701 C 3 .., III +chrM 702 A 3 .., III +chrM 703 G 3 .., 2II +chrM 704 C 3 .., III +chrM 705 A 3 N., "II +chrM 706 A 3 .., I5I +chrM 707 A 3 .$., GII +chrM 708 C 2 ., II +chrM 709 C 2 ., II +chrM 710 C 2 ., II +chrM 711 T 2 ., II +chrM 712 A 2 .$, II +chrM 713 A 1 , I +chrM 714 A 1 , I +chrM 715 C 1 , I +chrM 716 A 1 , I +chrM 717 A 1 , I +chrM 718 G 1 , I +chrM 719 G 2 ,^:, I& +chrM 720 T 2 ,g I$ +chrM 721 A 2 ,, I3 +chrM 722 C 2 ,, I$ +chrM 723 C 2 ,t I& +chrM 724 G 2 ,, I) +chrM 725 A 2 ,, II +chrM 726 A 3 ,,^:. III +chrM 727 G 3 ,,. III +chrM 728 T 3 ,$,. III +chrM 729 A 2 ,. II +chrM 730 A 2 n. "I +chrM 731 G 2 ,. II +chrM 732 C 3 a.^:. $II +chrM 733 A 3 ,.. III +chrM 734 C 3 ,.. %II +chrM 735 A 3 ,.. III +chrM 736 A 3 ,.. *II +chrM 737 A 3 ,.. III +chrM 738 T 3 ,.. III +chrM 739 A 3 ,.. III +chrM 740 T 3 ,.. III +chrM 741 C 3 ,.. III +chrM 742 C 3 ,.. III +chrM 743 A 3 ,.. III +chrM 744 A 3 ,.. III +chrM 745 C 3 ,.. III +chrM 746 A 3 ,.. IIE +chrM 747 T 3 ,.. III +chrM 748 A 3 ,.. III +chrM 749 A 3 ,.. III +chrM 750 A 3 ,.. III +chrM 751 A 3 ,.. IAI +chrM 752 A 3 ,.. III +chrM 753 C 3 ,.. III +chrM 754 G 3 ,$.. III +chrM 755 T 2 .. II +chrM 756 T 3 ..^:, III +chrM 757 A 3 .., III +chrM 758 G 3 .., III +chrM 759 G 3 .., III +chrM 760 T 3 .., =II +chrM 761 C 3 .$., IID +chrM 762 A 2 ., =I +chrM 763 A 2 ., EI +chrM 764 G 2 ., II +chrM 765 G 2 ., II +chrM 766 T 2 ., :I +chrM 767 G 3 .$,^:, III +chrM 768 T 2 ,, I> +chrM 769 A 3 ,,^:, III +chrM 770 G 3 ,,, III +chrM 771 C 3 ,,, IHI +chrM 772 C 3 ,a, I)/ +chrM 773 C 3 ,,, I7I +chrM 774 A 4 ,,,^:. II:I +chrM 775 T 4 ,,,. IH.I +chrM 776 G 4 ,,,. IIII +chrM 777 G 4 ,,,. IIII +chrM 778 G 4 ,,,. IIII +chrM 779 A 4 ,,,. IIAI +chrM 780 T 4 ,,,. IIGI +chrM 781 G 4 ,,,. IIII +chrM 782 G 4 ,,,. IIII +chrM 783 A 4 ,,,. IIII +chrM 784 G 4 ,,,. IIII +chrM 785 A 4 ,,,. IIII +chrM 786 G 4 ,,,. IIII +chrM 787 A 4 ,,,. IIII +chrM 788 A 4 ,,,. IIII +chrM 789 A 4 ,,,. IIII +chrM 790 T 5 ,,,.^:. IIIII +chrM 791 G 5 ,$,,.. IIIII +chrM 792 G 4 ,,.. IIII +chrM 793 G 4 ,,.. IIII +chrM 794 C 4 ,,.. IIII +chrM 795 T 4 ,,.. IIII +chrM 796 A 4 ,,.. IIII +chrM 797 C 4 ,,.. IIII +chrM 798 A 4 ,,.. IIII +chrM 799 T 4 ,,.. IIII +chrM 800 T 4 ,,.. IIII +chrM 801 T 4 ,,.. IIII +chrM 802 T 4 ,$,.. IIII +chrM 803 C 3 ,.. III +chrM 804 T 3 ,$.. III +chrM 805 A 2 .. II +chrM 806 C 3 ..^:. III +chrM 807 C 3 ... III +chrM 808 C 3 ... III +chrM 809 T 3 .$.. III +chrM 810 A 3 ..^:, III +chrM 811 A 3 .., III +chrM 812 G 3 .., II7 +chrM 813 A 3 .., III +chrM 814 A 3 .., III +chrM 815 C 3 .., III +chrM 816 A 3 .., III +chrM 817 A 3 .., III +chrM 818 G 3 .., III +chrM 819 A 3 .., III +chrM 820 A 3 .., &II +chrM 821 C 3 .., III +chrM 822 T 3 .., III +chrM 823 T 3 ..n II" +chrM 824 T 3 .., III +chrM 825 A 3 .$., III +chrM 826 A 3 .,^:. III +chrM 827 C 3 .,. III +chrM 828 C 3 .,. III +chrM 829 C 4 .,.^:, IIII +chrM 830 G 4 .,., IIII +chrM 831 G 4 .,., IIII +chrM 832 A 4 .,., IIII +chrM 833 C 4 .,., IIII +chrM 834 G 4 .,., IIII +chrM 835 A 4 .,., IIII +chrM 836 A 4 .,., 8III +chrM 837 A 4 .,., IIII +chrM 838 G 4 .,., IIII +chrM 839 T 5 .,.,^:, 4:IIG +chrM 840 C 5 .,.,, IIIII +chrM 841 T 5 .$,.,, IIIII +chrM 842 C 4 ,.,, IIII +chrM 843 C 4 ,.,, IIII +chrM 844 A 4 ,.,, IIII +chrM 845 T 4 ,$.,, IIII +chrM 846 G 3 .,, @II +chrM 847 A 3 .,, III +chrM 848 A 3 .,, III +chrM 849 A 3 .,, III +chrM 850 C 3 .,, III +chrM 851 T 3 .,, III +chrM 852 G 3 .,, III +chrM 853 G 3 .,, III +chrM 854 A 3 .,, EII +chrM 855 G 3 .,, DII +chrM 856 A 3 .,, III +chrM 857 C 3 .,, III +chrM 858 T 4 .,,^:, IIIA +chrM 859 A 4 .,,, @III +chrM 860 A 4 .,,, IIII +chrM 861 A 4 .$,,, EIII +chrM 862 G 3 ,,, III +chrM 863 G 3 ,,, III +chrM 864 A 3 ,$,, III +chrM 865 G 2 ,, II +chrM 866 G 2 ,, II +chrM 867 A 2 ,, II +chrM 868 T 2 ,, II +chrM 869 T 2 ,, II +chrM 870 T 2 ,, II +chrM 871 A 2 ,, II +chrM 872 G 2 ,, II +chrM 873 C 2 ,, II +chrM 874 A 2 ,$, II +chrM 875 G 1 , I +chrM 876 T 1 , I +chrM 877 A 1 , I +chrM 878 A 1 , I +chrM 879 A 1 , I +chrM 880 T 1 , I +chrM 881 T 1 , I +chrM 882 A 1 , I +chrM 883 A 1 , I +chrM 884 G 1 , I +chrM 885 A 1 , I +chrM 886 A 1 , I +chrM 887 T 1 , ( +chrM 888 A 1 , I +chrM 889 G 1 , I +chrM 890 A 1 , I +chrM 891 G 1 , I +chrM 892 A 1 , I +chrM 893 G 1 ,$ I +chrM 898 A 1 ^:, I +chrM 899 T 2 ,^:. /I +chrM 900 T 2 ,. 7I +chrM 901 G 2 ,. CI +chrM 902 A 2 ,. II +chrM 903 A 2 ,. II +chrM 904 T 2 ,. II +chrM 905 C 3 ,.^:, III +chrM 906 A 3 ,., III +chrM 907 G 3 ,., III +chrM 908 G 3 ,., III +chrM 909 C 3 ,., III +chrM 910 C 3 ,., III +chrM 911 A 4 ,.,^:, IIII +chrM 912 T 4 ,.,, IIEG +chrM 913 G 4 ,.,, III: +chrM 914 A 4 ,.,, IIII +chrM 915 A 4 ,.,, IIII +chrM 916 G 4 ,.,, III5 +chrM 917 C 4 ,.,, III5 +chrM 918 G 4 ,.,, IIII +chrM 919 C 4 ,.,, III< +chrM 920 G 4 ,.,, IIII +chrM 921 C 4 ,.,, IIII +chrM 922 A 4 ,.,, IIII +chrM 923 C 4 ,.,, III8 +chrM 924 A 4 ,.,, IFII +chrM 925 C 4 ,.,, IIII +chrM 926 A 4 ,.,, IIII +chrM 927 C 4 ,.,, IIII +chrM 928 C 5 ,.,,^:, IIII: +chrM 929 G 5 ,.,,, IIIE: +chrM 930 C 5 ,.,,, IIIII +chrM 931 C 5 ,.,,, IIIIF +chrM 932 C 5 ,.,,, IIIIC +chrM 933 G 5 ,$.,,, I?II: +chrM 934 T 4 .$,,, 4II> +chrM 935 C 3 ,,, III +chrM 936 A 3 ,,, III +chrM 937 C 3 ,,, II1 +chrM 938 C 3 ,,, III +chrM 939 C 3 ,,, III +chrM 940 T 3 ,$,, III +chrM 941 C 2 ,, II +chrM 942 C 2 ,, I' +chrM 943 T 2 ,, II +chrM 944 T 2 ,, II +chrM 945 A 2 ,, II +chrM 946 A 2 ,$, II +chrM 947 A 1 , I +chrM 948 T 1 , I +chrM 949 A 1 , I +chrM 950 T 1 , I +chrM 951 C 1 , I +chrM 952 A 1 , I +chrM 953 C 1 , I +chrM 954 A 1 , I +chrM 955 A 2 ,^:. II +chrM 956 A 2 ,. II +chrM 957 T 2 ,. II +chrM 958 C 3 ,.^:. III +chrM 959 A 3 ,.. III +chrM 960 T 3 ,.. III +chrM 961 A 3 ,.. III +chrM 962 A 3 ,.. III +chrM 963 C 4 ,$..^:. IIII +chrM 964 A 3 ... I(; +chrM 965 T 3 ... III +chrM 966 A 4 ...^:. IIII +chrM 967 A 4 .... IIII +chrM 968 C 4 .... IEII +chrM 969 A 4 .... IIII +chrM 970 T 4 .... IIII +chrM 971 A 4 .... IIII +chrM 972 A 4 .... IIII +chrM 973 A 4 .... II0I +chrM 974 A 5 ....^:. IIIII +chrM 975 C 5 ..... IIIII +chrM 976 C 5 ..... IIIII +chrM 977 G 5 ..... IIIII +chrM 978 T 5 ..... IIIII +chrM 979 G 5 ..... I0III +chrM 980 A 5 ..... IIII4 +chrM 981 C 5 ..... IIIII +chrM 982 C 5 ..... IIIII +chrM 983 C 5 ..... IIIII +chrM 984 A 5 ..... -IGII +chrM 985 A 5 ..... 4GIII +chrM 986 A 5 ..... BDGII +chrM 987 C 5 ..... IDIII +chrM 988 A 5 ..... @<III +chrM 989 T 5 ..... IIIII +chrM 990 A 5 .$.... I@III +chrM 991 T 4 .... IICI +chrM 992 G 4 T... )III +chrM 993 A 4 .$... ?ICI +chrM 994 A 3 ... III +chrM 995 A 3 ... III +chrM 996 G 3 ... III +chrM 997 G 3 ... III +chrM 998 A 3 .$.. 4II +chrM 999 G 3 ..^:. III +chrM 1000 A 3 ... III +chrM 1001 C 3 .$.. III +chrM 1002 A 2 .. II +chrM 1003 A 2 .. II +chrM 1004 G 2 .. II +chrM 1005 T 2 .. II +chrM 1006 C 2 .. II +chrM 1007 G 2 .. CI +chrM 1008 T 2 .. II +chrM 1009 A 2 .$. II +chrM 1010 A 1 . I +chrM 1011 C 1 . I +chrM 1012 A 1 . I +chrM 1013 A 1 . I +chrM 1014 G 1 . I +chrM 1015 G 1 . I +chrM 1016 T 1 . I +chrM 1017 A 1 . I +chrM 1018 A 1 . I +chrM 1019 G 1 . I +chrM 1020 T 1 . I +chrM 1021 A 1 . I +chrM 1022 T 1 . I +chrM 1023 A 1 . I +chrM 1024 C 1 . I +chrM 1025 C 1 . I +chrM 1026 G 1 . I +chrM 1027 G 1 . I +chrM 1028 A 1 . I +chrM 1029 A 1 . I +chrM 1030 G 1 . I +chrM 1031 G 2 .^:. II +chrM 1032 T 2 .. EI +chrM 1033 G 2 .. II +chrM 1034 T 2 .$. II +chrM 1035 A 2 .^:. II +chrM 1036 C 2 .. II +chrM 1037 T 2 .. II +chrM 1038 T 2 .. II +chrM 1039 G 2 .. II +chrM 1040 G 2 .. II +chrM 1041 A 2 .. II +chrM 1042 T 2 .. II +chrM 1043 A 3 ..^:, III +chrM 1044 A 3 .., III +chrM 1045 C 3 .., II7 +chrM 1046 C 3 .., II- +chrM 1047 A 3 .., III +chrM 1048 A 3 .., III +chrM 1049 A 3 .., III +chrM 1050 G 3 .., III +chrM 1051 T 3 .., III +chrM 1052 G 3 .., III +chrM 1053 T 3 .., GII +chrM 1054 A 3 .., III +chrM 1055 G 3 .., :II +chrM 1056 C 3 ..a HI% +chrM 1057 T 3 .., III +chrM 1058 T 3 .., III +chrM 1059 A 3 .., BII +chrM 1060 A 3 .., GII +chrM 1061 A 3 .., HII +chrM 1062 C 3 .., III +chrM 1063 A 3 .., DII +chrM 1064 A 3 .., BII +chrM 1065 A 3 .., 1II +chrM 1066 G 3 .$., &II +chrM 1067 C 2 ., II +chrM 1068 A 2 ., II +chrM 1069 T 2 ., II +chrM 1070 C 2 .$, II +chrM 1071 C 1 , I +chrM 1072 A 1 , I +chrM 1073 G 1 , I +chrM 1074 C 1 , I +chrM 1075 T 1 , I +chrM 1076 T 1 , I +chrM 1077 A 1 , I +chrM 1078 C 1 ,$ I +chrM 1090 T 1 ^:, I +chrM 1091 T 1 , I +chrM 1092 C 1 n " +chrM 1093 A 1 , I +chrM 1094 C 1 , I +chrM 1095 T 1 , 7 +chrM 1096 C 1 a B +chrM 1097 A 1 , I +chrM 1098 A 1 , I +chrM 1099 A 1 , I +chrM 1100 A 1 , I +chrM 1101 T 1 , I +chrM 1102 G 2 ,^:, (I +chrM 1103 A 2 ,, II +chrM 1104 A 2 ,, I+ +chrM 1105 C 2 ,, .I +chrM 1106 A 2 ,, 8I diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in1.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,30 @@ +chrM 1 A G 25 0 25 1 ^:. I +chrM 2 C T 25 0 25 2 .N I$ +chrM 3 T G 27 0 25 2 .. II +chrM 4 G C 36 0 25 3 .^:.^:. II+ +chrM 5 T A 38 0 25 3 ... III +chrM 6 T A 39 0 25 4 .N.. I$II +chrM 7 G C 43 0 25 5 ...^:.^:. IIIII +chrM 8 A C 46 0 25 6 .....^:. IIIIII +chrM 9 T G 53 0 25 8 ..G...^:.^:. IIIII$II +chrM 10 T G 56 0 25 9 ........^:. IIIIIIIII +chrM 11 C G 57 0 25 10 .........^:. IIIIIIIIII +chrM 12 T C 61 0 25 11 ..........^:. IIIIIIIIIII +chrM 13 T G 79 0 25 15 .........^:.^:.^:.^:.^:.^:. IIIIIIIIIIII#II +chrM 14 A C 58 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII +chrM 15 G A 87 0 25 19 ..N...............^:.^:. DIIIIII$(IIIIIIIIIII +chrM 16 G C 88 0 25 20 .........N.......... IIIIIIIIIIIIIIIIIIII +chrM 17 A C 88 0 25 20 .........G.......... 9IIIIIIIIIIIIIIIIIII +chrM 18 G A 89 0 25 20 ...A................ @IIIIIIIIIIIIIIIIIII +chrM 19 G T 58 0 25 20 ....T.............GG IIIIIIIIIIIIIIIIII'A +chrM 20 T C 55 0 25 20 .........C........C. IIIIIIIIIIIIIII2II#$ +chrM 21 C T 87 0 25 20 ..........G......... IIIIIIIIIIIIIIIIIIII +chrM 22 C A 87 0 25 20 ..........N......... IIIIIIIIIIIIIIAIIIII +chrM 23 A G 87 0 25 20 .....T.............. 9IIIIIIIIII0IIIIIIII +chrM 24 A T 89 0 25 20 .....N..N........... III$IIII"IIIIICII#II +chrM 25 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII +chrM 26 C G 58 0 25 22 ...N....A............. IIHIDII&IIIIII@IIIIII +chrM 27 T A 99 0 25 23 ....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIII +chrM 28 A C 99 0 25 24 ..G..................... 1FIIIIIIIIIIIIIIIIDEIIII +chrM 29 G C 58 0 25 25 ........C.........NN.... ;IIIIII+HII=III$III""IIII +chrM 30 T T 65 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in2.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in2.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,30 @@ +chrM 1 T G 25 0 25 1 ^:. I +chrM 2 C A 25 0 25 1 . I +chrM 3 C A 25 0 25 2 .. I+ +chrM 4 G A 36 0 25 3 .^:.^:. II+ +chrM 5 A T 36 0 25 3 ... IDI +chrM 6 A G 36 0 25 4 ..T. IIBI +chrM 7 C G 42 0 25 5 ...^:.^:. ID@II +chrM 8 T T 45 0 25 6 .....^:. III$BI +chrM 9 C A 51 0 25 8 ......^:.^:. $#III+III +chrM 10 G G 54 0 25 9 ........^:. III$III#I +chrM 11 T C 57 0 25 10 .........^:. IIIDBIIIII +chrM 12 A T 60 0 25 11 ..........^:. IIIIIIIII$I +chrM 13 A T 78 0 25 18 ..A.........^:.^:.^:.^:.^:.^:. III#$IIIIII+IIDIIB +chrM 14 G A 56 0 25 19 ........T.........^:. BIIIIIII+IIII$IBIII +chrM 15 G A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII +chr1 1 T T 87 0 25 20 .............T...... IIIIIIIIIIII$DIIIIII +chr1 2 A T 87 0 25 20 ......G............. 9IIIIIIIIIIIIICBIIII +chr1 3 A G 87 0 25 20 ....A............... @IIIIIIIII#IIII#IIII +chr1 4 A T 55 0 25 20 ..................GG IIIII@II$IIIIIIIII'A +chr1 5 C A 54 0 25 20 .......A..........C. IIIIIIIIIDIIIII2II#$ +chr1 6 G T 87 0 25 20 .............A...... IIIIIIIBIIIIII#IIIII +chr1 7 A C 87 0 25 20 ..........C......... IIIII+IIIIIIIIAIIIII +chr1 8 G A 87 0 25 20 ....G.........T..... 9IIIIIIIIII0IIIIIIII +chr1 9 A T 87 0 25 20 ........N........... IIII$III"IIIIICIIIII +chr1 10 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII +chr1 11 C A 57 0 25 22 ....G...A............. IIHIDII&IIIIII#III$II +chr1 12 T A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII +chr1 13 A C 99 0 25 25 ...N..................... 1FIIIIIIIIIIIIIIIIDEII$II +chr1 14 G C 55 0 25 25 ....G..............NN.... ;IIIBIII+HII=IIIIII""IIII +chr1 15 T G 68 0 25 28 ...C.......N............^:. ;I?&IAI0IIIIIII@II#$II@II diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in3.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in3.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,30 @@ +chr1 1 G G 25 0 25 1 ^:. I +chr1 2 T T 25 0 25 1 . I +chr1 3 T T 27 0 25 1 . I +chr1 4 A A 36 0 25 2 .^:. I+ +chr1 5 A A 36 0 25 3 ... III +chr1 6 T T 36 0 25 4 .N.. II#I +chr1 7 G G 42 0 25 5 ...^:.^:. IIIII +chr1 8 T T 45 0 25 6 .....^:. IIIIII +chr1 9 A A 51 0 25 7 .....^:.^:. IBIIIII +chr1 10 G G 54 0 25 9 ........^:. IIIIIIIII +chr1 11 C C 57 0 25 10 .........^:. IIIIIIII"I +chr1 12 T T 60 0 25 11 ..........^:. IIIIIIDIIII +chr1 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIII"$IIIIIIIIIII +chr1 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII +chr1 15 A A 87 0 25 20 ....N.............^:.^:. DIII$III(IIIIIIIIIII +chr4 1 T T 90 0 25 20 ..........N......... IIIIIIIII$IIIIIIIIII +chr4 2 A A 87 0 25 20 .......C............ 9IIIIIIIII"IIIIIIIII +chr4 3 A A 34 0 25 20 ......G............. @IIIIIIIIIIII#IIIIII +chr4 4 T T 55 0 25 21 ...........N.......GG IIIII@IIIIIIIIIIIII'A +chr4 5 A A 54 0 25 21 ...N...............C. IIII"IIIIIIIIIII2II#$ +chr4 6 T T 87 0 25 21 ................N.... IIIIIIII$IIIIIIIIIIII +chr4 7 A A 80 0 25 21 .....G............... III$IIIIIIIIIIIAIIIII +chr4 8 A A 87 0 25 22 ..N................... 9IIIIIIIIII0IIIII"$III +chr4 9 A A 87 0 25 22 .GG.......N........... IIII$IIIII"IIIIICIIIII +chr4 10 G G 57 0 25 23 .....A................^:. A@.$IIIIIIIIIFIIIIIIIII +chr4 11 C C 57 0 25 25 .......A.....GN.......... IIHIDII&III#IIIIIIIIIIIII +chr4 12 A A 99 0 25 26 .......................^:.^:.^:. IE8IFIII9IIIIIII$IIIIIIIII +chr4 13 A A 99 0 25 27 ........N.................. 1FIIIIII$IIIIIIIIIIIIDEIIII +chr4 14 G G 55 0 25 28 ..N...................NN.... ;III$I#IIII+HII=IIIIII""IIII +chr4 15 G G 68 0 25 30 ...C....N..G.................^:. ;I?&IAI0IIIIIII$#I$@IIIIIIIIII diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in4.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in4.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,25 @@ +chr2 1 T 6 .C..., I$$III +chr2 2 G 6 ..N.., III@II +chr2 3 C 7 ..C..., I$IIIII +chr2 4 G 7 .G...., I#IIIII +chr2 5 G 7 ...N.., IIII#BI +chr2 6 A 7 ..T..., I$IDIII +chr2 7 T 8 ...C..., IIIBD$II +chr2 8 A 8 ..A...., IBI#IIII +chr2 9 C 9 .GA..N.., I$IBIII#I +chr2 10 T 9 ........, I$II#IIII +chr2 11 C 10 .>>..T..., IIII@I$I$I +chr2 12 G 10 .N..G...., III$IIIIII +chr2 13 A 11 ....A..T.., IIIIII#I@II +chr1 1 C 1 ^:. I +chr1 2 G 2 .^:. $I +chr1 3 A 2 .. I% +chr1 4 C 2 .. I$ +chr1 5 T 3 ..^:. I#I +chr1 6 G 3 ..^:, I#I +chr1 7 C 4 .N., IIII +chr1 8 A 4 ..., I$II +chr1 9 T 5 ..C., I#IDI +chr1 10 G 5 N..., IBII@ +chr1 11 A 5 .C.., I$II# +chr1 12 C 5 ..N., I$III diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in5.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in5.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,25 @@ +chr1 42 T 1 ^:. I +chr1 43 G 2 .^:. $I +chr1 44 T 2 .. I% +chr1 45 C 3 ..^:. III +chr1 46 G 3 ..^:. I#I +chr1 47 T 4 ...^:, I#II +chr1 48 A 4 .N., IIII +chr1 49 C 5 ...., IIIII +chr1 50 A 5 ..G., IIIDI +chr1 51 A 5 A..., IBIII +chr1 52 A 5 ...., IIII# +chr1 53 G 5 ..N., I$III +chr2 77 C 6 .G..., I$$III +chr2 78 G 6 ..N.., III@II +chr2 79 T 7 ..N..., I$IIIII +chr2 80 C 7 .G...., I#IIIII +chr2 81 G 7 ...A.., IIII#BI +chr2 82 A 8 ...G..., I$IDIIII +chr2 83 A 8 ...T..., IIIBD$II +chr2 84 T 8 ..A...., IBI#IIII +chr2 85 G 8 .GA...., IIBIII#I +chr2 86 C 9 ........, I$II#IIII +chr2 87 G 9 ....T..., IIIII$I$I +chr2 88 G 10 .N..G...., III$IIIIII +chr2 89 G 10 ...A..T.., IIIII#I@II diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in6.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in6.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,25 @@ +chr1 42 C 1 ^:. I +chr1 43 C 2 .^:. II +chr1 44 T 2 .. II +chr1 45 A 3 ..^:. III +chr1 46 G 4 ...^:. IIII +chr1 47 A 5 ....^:, IIIII +chr1 48 T 5 ...N, I#III +chr1 49 G 5 ...., IIIII +chr1 50 A 5 .G.., IIIII +chr1 51 G 5 ...., IIIII +chr2 52 T 5 .N.., II$II +chr2 53 A 5 ...., IIIII +chr2 54 T 5 ...., IIIII +chr2 55 T 5 ...., IIIII +chr2 56 C 5 ...., IIIBI +chr2 57 T 5 ...., IDIII +chr2 58 T 6 .N..., IIIIII +chr2 59 A 6 ....., IIII$I +chr3 60 C 6 ...G., I#IIII +chr3 61 T 6 ..N.., IIIIII +chr3 62 C 6 ...A., IIIIII +chr3 63 C 7 .N...., IIIIIII +chr3 64 A 7 ...G.., IIIII$I +chr3 65 T 7 ...AA., IIIII@@ +chr3 66 A 7 ....N., IIIIIII diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in7.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in7.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,32 @@ +chr2 1 T 6 .C..., I$$III +chr2 2 G 6 ..N.., III@II +chr2 3 C 7 ..C..., I$IIIII +chr2 4 G 7 .G...., I#IIIII +chr2 5 G 7 ...N.., IIII#BI +chr2 6 A 7 ..T..., I$IDIII +chr2 7 T 8 ...C..., IIIBD$II +chr2 8 A 8 ..A...., IBI#IIII +chr2 9 C 9 .GA..N.., I$IBIII#I +chr2 10 T 9 ........, I$II#IIII +chr2 11 C 10 .>>..T..., IIII@I$I$I +chr2 12 G 10 .N..G...., III$IIIIII +chr2 13 A 11 ....A..T.., IIIIII#I@II +chr2 14 G 11 ..N....... IICIBII@AII +chr2 15 C 11 A.....NG.. IIIIIDIIIII +chr2 16 T 11 ...C.....G I$IIIB@IIIC +chr2 17 C 12 G......TN.. IIAII@IIII$I +chr2 18 A 12 N......G..A IIIBIII$IIII +chr2 19 A 13 .......NN... IIIIIIBIII$$@ +chr2 20 C 13 ..GT.......N IIIIABIIC$III +chr1 1 C 1 ^:. I +chr1 2 G 2 .^:. $I +chr1 3 A 2 .. I% +chr1 4 C 2 .. I$ +chr1 5 T 3 ..^:. I#I +chr1 6 G 3 ..^:, I#I +chr1 7 C 4 .N., IIII +chr1 8 A 4 ..., I$II +chr1 9 T 5 ..C., I#IDI +chr1 10 G 5 N..., IBII@ +chr1 11 A 5 .C.., I$II# +chr1 12 C 5 ..N., I$III diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in8.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in8.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,23 @@ +chr1 42 T 1 ^:. I +chr1 43 G 2 .^:. $I +chr1 44 T 2 .. I% +chr1 45 C 3 ..^:. III +chr1 46 G 3 ..^:. I#I +chr1 47 T 4 ...^:, I#II +chr1 48 A 4 .N., IIII +chr1 49 C 5 ...., IIIII +chr1 50 A 5 ..G., IIIDI +chr1 51 A 5 A..., IBIII +chr1 52 A 5 ...., IIII# +chr1 53 G 5 ..N., I$III +chr2 77 C 6 .G..., I$$III +chr2 78 G 6 ..N.., III@II +chr2 79 T 7 ..N..., I$IIIII +chr2 80 C 7 .G...., I#IIIII +chr2 81 G 7 ...A.., IIII#BI +chr2 82 A 8 ...G..., I$IDIIII +chr2 83 A 8 ...T..., IIIBD$II +chr2 84 T 8 ..A...., IBI#IIII +chr2 85 G 8 .GA...., IIBIII#I +chr2 86 C 9 ........, I$II#IIII +chr2 87 G 9 ....T..., IIIII$I$I diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_in9.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_in9.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,25 @@ +chr1 43 C 2 .^:. II +chr3 65 T 7 ...AA., IIIII@@ +chr1 44 T 2 .. II +chr2 54 T 5 ...., IIIII +chr1 45 A 3 ..^:. III +chr1 47 A 5 ....^:, IIIII +chr1 50 A 5 .G.., IIIII +chr1 51 G 5 ...., IIIII +chr2 52 T 5 .N.., II$II +chr2 53 A 5 ...., IIIII +chr3 60 C 6 ...G., I#IIII +chr3 61 T 6 ..N.., IIIIII +chr1 49 G 5 ...., IIIII +chr2 55 T 5 ...., IIIII +chr2 56 C 5 ...., IIIBI +chr2 58 T 6 .N..., IIIIII +chr2 59 A 6 ....., IIII$I +chr3 62 C 6 ...A., IIIIII +chr1 42 C 1 ^:. I +chr3 63 C 7 .N...., IIIIIII +chr1 48 T 5 ...N, I#III +chr1 46 G 4 ...^:. IIII +chr3 64 A 7 ...G.., IIIII$I +chr3 66 A 7 ....N., IIIIIII +chr2 57 T 5 ...., IDIII diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out1.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_out1.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,60 @@ +chr1 1 T T 87 25 G G 25 25 +chr1 2 A T 87 25 T T 25 25 +chr1 3 A G 87 25 T T 27 25 +chr1 4 A T 55 25 A A 36 25 +chr1 5 C A 54 25 A A 36 25 +chr1 6 G T 87 25 T T 36 25 +chr1 7 A C 87 25 G G 42 25 +chr1 8 G A 87 25 T T 45 25 +chr1 9 A T 87 25 A A 51 25 +chr1 10 G A 57 25 G G 54 25 +chr1 11 C A 57 25 C C 57 25 +chr1 12 T A 99 25 T T 60 25 +chr1 13 A C 99 25 T T 78 25 +chr1 14 G C 55 25 A A 56 25 +chr1 15 T G 68 25 A A 87 25 +chr4 1 T T 90 25 +chr4 2 A A 87 25 +chr4 3 A A 34 25 +chr4 4 T T 55 25 +chr4 5 A A 54 25 +chr4 6 T T 87 25 +chr4 7 A A 80 25 +chr4 8 A A 87 25 +chr4 9 A A 87 25 +chr4 10 G G 57 25 +chr4 11 C C 57 25 +chr4 12 A A 99 25 +chr4 13 A A 99 25 +chr4 14 G G 55 25 +chr4 15 G G 68 25 +chrM 1 A G 25 25 T G 25 25 +chrM 2 C T 25 25 C A 25 25 +chrM 3 T G 27 25 C A 25 25 +chrM 4 G C 36 25 G A 36 25 +chrM 5 T A 38 25 A T 36 25 +chrM 6 T A 39 25 A G 36 25 +chrM 7 G C 43 25 C G 42 25 +chrM 8 A C 46 25 T T 45 25 +chrM 9 T G 53 25 C A 51 25 +chrM 10 T G 56 25 G G 54 25 +chrM 11 C G 57 25 T C 57 25 +chrM 12 T C 61 25 A T 60 25 +chrM 13 T G 79 25 A T 78 25 +chrM 14 A C 58 25 G A 56 25 +chrM 15 G A 87 25 G A 87 25 +chrM 16 G C 88 25 +chrM 17 A C 88 25 +chrM 18 G A 89 25 +chrM 19 G T 58 25 +chrM 20 T C 55 25 +chrM 21 C T 87 25 +chrM 22 C A 87 25 +chrM 23 A G 87 25 +chrM 24 A T 89 25 +chrM 25 G A 57 25 +chrM 26 C G 58 25 +chrM 27 T A 99 25 +chrM 28 A C 99 25 +chrM 29 G C 58 25 +chrM 30 T T 65 25 diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out2.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_out2.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,65 @@ +chr1 1 C 1 +chr1 2 G 2 +chr1 3 A 2 +chr1 4 C 2 +chr1 5 T 3 +chr1 6 G 3 +chr1 7 C 4 +chr1 8 A 4 +chr1 9 T 5 +chr1 10 G 5 +chr1 11 A 5 +chr1 12 C 5 +chr1 42 T 1 C 1 +chr1 43 G 2 C 2 +chr1 44 T 2 T 2 +chr1 45 C 3 A 3 +chr1 46 G 3 G 4 +chr1 47 T 4 A 5 +chr1 48 A 4 T 5 +chr1 49 C 5 G 5 +chr1 50 A 5 A 5 +chr1 51 A 5 G 5 +chr1 52 A 5 +chr1 53 G 5 +chr2 1 T 6 +chr2 2 G 6 +chr2 3 C 7 +chr2 4 G 7 +chr2 5 G 7 +chr2 6 A 7 +chr2 7 T 8 +chr2 8 A 8 +chr2 9 C 9 +chr2 10 T 9 +chr2 11 C 10 +chr2 12 G 10 +chr2 13 A 11 +chr2 52 T 5 +chr2 53 A 5 +chr2 54 T 5 +chr2 55 T 5 +chr2 56 C 5 +chr2 57 T 5 +chr2 58 T 6 +chr2 59 A 6 +chr2 77 C 6 +chr2 78 G 6 +chr2 79 T 7 +chr2 80 C 7 +chr2 81 G 7 +chr2 82 A 8 +chr2 83 A 8 +chr2 84 T 8 +chr2 85 G 8 +chr2 86 C 9 +chr2 87 G 9 +chr2 88 G 10 +chr2 89 G 10 +chr3 60 C 6 +chr3 61 T 6 +chr3 62 C 6 +chr3 63 C 7 +chr3 64 A 7 +chr3 65 T 7 +chr3 66 A 7 diff -r 5f927f52191c -r 3ac95cd927d7 test-data/column_join_out3.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/column_join_out3.pileup Fri Mar 26 12:00:55 2010 -0400 @@ -0,0 +1,70 @@ +chr1 1 C 1 ^:. +chr1 2 G 2 .^:. +chr1 3 A 2 .. +chr1 4 C 2 .. +chr1 5 T 3 ..^:. +chr1 6 G 3 ..^:, +chr1 7 C 4 .N., +chr1 8 A 4 ..., +chr1 9 T 5 ..C., +chr1 10 G 5 N..., +chr1 11 A 5 .C.., +chr1 12 C 5 ..N., +chr1 42 T 1 ^:. C 1 ^:. +chr1 43 G 2 .^:. C 2 .^:. +chr1 44 T 2 .. T 2 .. +chr1 45 C 3 ..^:. A 3 ..^:. +chr1 46 G 3 ..^:. G 4 ...^:. +chr1 47 T 4 ...^:, A 5 ....^:, +chr1 48 A 4 .N., T 5 ...N, +chr1 49 C 5 ...., G 5 ...., +chr1 50 A 5 ..G., A 5 .G.., +chr1 51 A 5 A..., G 5 ...., +chr1 52 A 5 ...., +chr1 53 G 5 ..N., +chr2 1 T 6 .C..., +chr2 2 G 6 ..N.., +chr2 3 C 7 ..C..., +chr2 4 G 7 .G...., +chr2 5 G 7 ...N.., +chr2 6 A 7 ..T..., +chr2 7 T 8 ...C..., +chr2 8 A 8 ..A...., +chr2 9 C 9 .GA..N.., +chr2 10 T 9 ........, +chr2 11 C 10 .>>..T..., +chr2 12 G 10 .N..G...., +chr2 13 A 11 ....A..T.., +chr2 14 G 11 ..N....... +chr2 15 C 11 A.....NG.. +chr2 16 T 11 ...C.....G +chr2 17 C 12 G......TN.. +chr2 18 A 12 N......G..A +chr2 19 A 13 .......NN... +chr2 20 C 13 ..GT.......N +chr2 52 T 5 .N.., +chr2 53 A 5 ...., +chr2 54 T 5 ...., +chr2 55 T 5 ...., +chr2 56 C 5 ...., +chr2 57 T 5 ...., +chr2 58 T 6 .N..., +chr2 59 A 6 ....., +chr2 77 C 6 .G..., +chr2 78 G 6 ..N.., +chr2 79 T 7 ..N..., +chr2 80 C 7 .G...., +chr2 81 G 7 ...A.., +chr2 82 A 8 ...G..., +chr2 83 A 8 ...T..., +chr2 84 T 8 ..A...., +chr2 85 G 8 .GA...., +chr2 86 C 9 ........, +chr2 87 G 9 ....T..., +chr3 60 C 6 ...G., +chr3 61 T 6 ..N.., +chr3 62 C 6 ...A., +chr3 63 C 7 .N...., +chr3 64 A 7 ...G.., +chr3 65 T 7 ...AA., +chr3 66 A 7 ....N., diff -r 5f927f52191c -r 3ac95cd927d7 test/functional/test_get_data.py --- a/test/functional/test_get_data.py Fri Mar 26 09:51:03 2010 -0400 +++ b/test/functional/test_get_data.py Fri Mar 26 12:00:55 2010 -0400 @@ -575,5 +575,22 @@ self.check_history_for_string( 'Pasted Entry' ) self.check_history_for_string( 'hello world' ) self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0165_upload_file( self ): + """Test uploading 1.pileup, NOT setting the file format""" + self.check_history_for_string( 'Your history is empty' ) + history = sa_session.query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + self.upload_file( '1.pileup' ) + hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ + .first() + assert hda is not None, "Problem retrieving hda from database" + self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) ) + self.check_history_for_string( '1.pileup format: <span class="pileup">pileup</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' ) + self.delete_history( id=self.security.encode_id( history.id ) ) def test_9999_clean_up( self ): self.logout() diff -r 5f927f52191c -r 3ac95cd927d7 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Mar 26 09:51:03 2010 -0400 +++ b/tool_conf.xml.sample Fri Mar 26 12:00:55 2010 -0400 @@ -61,6 +61,7 @@ <tool file="filters/compare.xml"/> <tool file="new_operations/subtract_query.xml"/> <tool file="stats/grouping.xml" /> + <tool file="new_operations/column_join.xml" /> </section> <section name="Convert Formats" id="convert"> <tool file="filters/axt_to_concat_fasta.xml" />