1[2.0.13] 2- Fixed a bug that caused invalid bit scores in frameshift alignment mode. 3 4[2.0.12] 5- Fixed an error when using HSP filter settings together with a BLAST database. 6- Optimized the performance of alignment traceback. 7- A non-default setting of `--max-hsps` will now recompute a full-matrix Smith Waterman 8 alignment with the ranges of the known HSPs masked in the target. 9- A non-default setting for `--max-hsps` can now be used together with `--ext full`. 10- The sensitivity levels used for iterated searches can now be manually set by 11 using a space-separated list after the `--iterate` option. 12- Seeds are masked based on complexity instead of frequency by default. 13- Added the option `--seed-cut` to set a complexity cutoff for indexed seeds. 14- Added the option `--freq-masking` to enable masking seeds based on frequency. 15- The fast, default, mid-sensitive and sensitive modes will by default softmask 16 a fixed set of highly abundant sequence motifs. 17- Added the option `--motif-masking (0,1)` to enable or disable motif masking. 18- Added the option `--masking seg` to enable SEG masking of target sequences (BLAST 19 default) instead of tantan masking. 20- Fixed a bug that caused the `full_sseq` output field to contain invalid information 21 or to produce an error when using a BLAST database. 22- Changed composition based statistics to use BLOSUM62 background frequencies. 23- Fixed the zstd dependency in the Dockerfile. 24- Added support for gap letters in BLAST databases. 25- Fixed a bug that caused the `--custom-matrix` option not to function correctly. 26- Changed the overlap for merging adjoining bands to >0.0. 27- Use more moderate filtering of HPSs in the chaining stage. 28 29[2.0.11] 30- Fixed a bug that could cause invalid output when using `--masking 0` combined with 31 the global ranking mode. 32- Enabled lazy repeat masking in the query-indexed and contiguous seed modes when 33 using global ranking. 34- Added detection of cache size to auto-enable query-indexed mode. 35 36[2.0.10] 37- Using BLAST databases now requires a preprocessing step using the command `prepdb`. 38- Improved performance of searching small query files. 39- Added "iterative" search mode (option `--iterate`) to search the query dataset with 40 increasing sensitivity, only searching queries at the target sensitivity that fail 41 to align at a lower sensitivity search. 42- Added the "global ranking" mode (option `-g`) to set a limit on the number of 43 Smith Waterman extensions per query, with the target sequences ranked by their 44 ungapped extension scores. 45- Added the `--fast` sensitivity mode that is faster and less sensitive than the 46 default mode. 47- Reduced the time for loading target sequences from BLAST databases. 48- Added the contiguous-seed mode (option `--algo ctg`) to improve performance for 49 small query files. 50- Added support for using `--comp-based-stats (3,4)` in combination with `--ext full`. 51- Fixed a bug that could cause a `Traceback error` when using `--comp-based-stats (3,4)` 52 in rare cases. 53- Changed the `full_sseq` output field to always contain unmasked sequences. 54- Fixed an issue that could cause target output order to be nondeterministic in case 55 of identically scoring hits. 56- Added support for reading zstd-compressed input files (auto-detected) and writing 57 zstd-compressed output files (option `--compress zstd`) (requires compilation 58 using `cmake -DWITH_ZSTD=ON`). 59- Compilation with BLAST database support requires the zstd library. 60- Added error message when reading protein sequences from FASTA files that only 61 contain DNA letters (can be disabled using `--ignore-warnings`). 62 63[2.0.9] 64- Reduced the memory use of database building with taxonomy mapping. 65- Removed the limitation of sequence accession length. 66- Fixed a bug that could cause using a BLAST database not to function correctly. 67- Added support for using BLAST alias databases (created by `blastdb_aliastool`). 68- Reduced the memory use of the seed hit sorting stage. 69- Improved the consistency of results when running in query-indexed mode (`--algo 1`). 70- Added the option `--skip-missing-seqids` to ignore cases of missing sequences 71 in the database when using the `--seqidlist` option. 72- The `--min-orf` parameter now defaults to 1 in frameshift alignment mode. 73 74[2.0.8] 75- Added support for using BLAST database files instead of the Diamond-formatted 76 `.dmnd` files. 77- Added the option `--seqidlist` to filter the database by sequence accession (only 78 supported for BLAST databases). 79- Fixed a bug that caused the `--dbsize` option not to function correctly. 80- Added the command `makeidx` and the option `--target-indexed` that provide an 81 optimisation specialized for small databases (<10 Mb). 82- Added the option `--mp-recover` to recover aborted runs in multiprocessing mode. 83 84[2.0.7] 85- Added support for computing full-matrix instead of banded Smith Waterman extensions 86 (command line option `--ext full`). 87- Added support for the new `prot.accession2taxid.FULL.gz` taxonomy mapping file from 88 NCBI. 89- Added the option `--gapped-filter-evalue` to set the e-value threshold of the gapped 90 filter heuristic. 91- Added setting the scores of the mask letter according to BLAST rules when a 92 compositionally adjusted matrix is used. 93- Changed formatting of e-values to print two decimals instead of one. 94- Added the output field `qseq_translated` to print the translation of the aligned part 95 of the query sequence. 96- Added support for providing two input files to `--query/-q` when running alignment 97 in blastx mode. 98- Added the output field `full_qseq_mate` to print the sequence of the query's mate 99 (enabled when using two query files in blastx mode). 100- Fixed a bug that could cause a crash in blastx mode for very long queries. 101 102[2.0.6] 103- Changed the computation of expected values to use the method described in Park, Y., 104 Sheetlin, S., Ma, N. et al. New finite-size correction for local alignment score 105 distributions. *BMC Res Notes* **5**, 286 (2012). 106- Enabled the use of a custom scoring matrix without having to specify the statistical 107 parameters (option `--custom-matrix`). 108- Added support for compositional matrix adjust as described in Yi-Kuo Yu, Stephen F. 109 Altschul, The construction of amino acid substitution matrices for the comparison of 110 proteins with non-standard compositions, *Bioinformatics*, Volume 21, Issue 7, 1 April 111 2005, Pages 902�911. Three additional modes have been added that can be enabled by 112 setting `--comp-based-stats (2,3,4)` (*the feature is not enabled by default and does 113 not support translated searches at the moment*). 114- Fixed a bug that could cause incorrect alignment coordinates, gaps counts and sequence 115 identities being reported by `diamond view`. 116- Targets are sorted by bit score instead of e-value in the alignment output when the 117 `--top` parameter is used. 118- Disabled support of custom scoring matrices for the DAA format. 119- Fixed a bug that caused the use of a custom scoring matrix not to function correctly. 120- Fixed an issue that caused the portable binary not to function on systems that did not 121 support AVX. 122- Added the option `--no-unlink` to prevent unlinking of temporary files. 123 124[2.0.5] 125- Fixed an issue that could cause high memory use in frameshift alignment mode. 126 127[2.0.4] 128- Fixed a bug that could cause the `--max-target-seqs/-k`, `--ext-chunk-size` and 129 `--file-buffer-size` options not to function correctly on macOS. 130 131[2.0.3] 132- Added a new sensitivity mode that is between the default mode and the sensitive mode 133 in sensitivity (option `--mid-sensitive`). 134- Added counters for total number of reference blocks, shapes and index chunks to 135 the status messages. 136- Fixed a bug (persisting since v2.0.2) that could cause secondary HSPs within one 137 target not to be reported if the `--max-hsps` option was used with a non-default setting. 138- Fixed a bug that could cause an invalid error message with regard to the database 139 format in certain cases. 140- The `--no-self-hits` option is no longer supported in `blastx` mode. 141- Changed the semantics of the `--no-self-hits` option to check for equality of both 142 sequence and sequence id, independent of the computed alignment. 143- The selection of the top hit when using `--top` will respect the identity, coverage 144 and no-self-hits filter settings (does not apply when frameshift alignment is 145 enabled). 146- The inclusion criterion for `--top` is applied to the bit score instead of the raw 147 score and is no longer affected by integer rounding (does not apply when frameshift 148 alignment is enabled). 149- Improved the accuracy of the ranking heuristic. 150- Added the options `--ext-chunk-size` and `--no-ranking` to control the ranking 151 heuristic. 152 153[2.0.2] 154- Fixed a bug (persisting since v2.0.0) that could cause incomplete results in `blastx` mode. 155- Reduced the use of temporary disk space. 156- Fixed an issue that could cause long runtimes when using the `--taxon-list` option. 157 158[2.0.1] 159- Added feature for using the tool in a distributed computing environment. 160- Fixed an issue that could cause increased memory usage and runtimes for very long queries. 161- Fixed a bug that could cause a crash when using `--comp-based-stats 0`. 162- Fixed a bug that could cause a crash for small input files in certain cases. 163- Fixed a bug that could cause filtering hits for identity or range cover not to function correctly when using 164 the tabular format without traceback being enabled. 165- Added warning messages to recommend block size parameters based on system RAM. 166 167[2.0.0] 168- Added the sensitivity modes `--very-sensitive` and `--ultra-sensitive`. 169- The `--block-size`/`-b` parameter is set to 0.4 and the `--index-chunks`/`-c` parameter is set to 1 by default 170 in the new sensitivity modes. 171- Improved performance. 172- Added the option `--ext` with possible values `banded-fast` and `banded-slow` to adjust band setup for Smith 173 Waterman extensions (new default is `banded-fast` for the default and sensitive mode, and `banded-slow` otherwise). 174- Added automatic disabling of alignment traceback if not required by the user-defined output fields in tabular 175 output format. 176- Changed the default value of the `--max-hsps` parameter to 1. 177- Changed the default value of the `--freq-sd` parameter from 10 to 20 for the sensitive mode. 178- Fixed a compiler error on FreeBSD. 179 180[0.9.36] 181- Fixed a bug that could cause `makedb` to produce invalid database files when using taxonomy features. 182- Fixed a bug that could cause a crash when running in query-indexed mode. 183 184[0.9.35] 185- Fixed a bug in `diamond view` that would cause high memory usage and erroneous output. 186- Reduced the use of temporary disk space. 187- Fixed a database compatibility issue with big endian architectures. 188- Fixed a bug that would cause a crash for query sequences shorter than 5 letters in blastx mode. 189- Fixed a bug that would cause a crash when using a FASTA file as database parameter in blastx mode. 190- Added support for the following new ranks in the NCBI taxonomy: biotype, clade, forma specialis, genotype, isolate, morph, pathogroup, serogroup, serotype, strain, subvariety. 191 192[0.9.34] 193- Fixed a compiler error for native builds. 194- Fixed a compiler error for GCC 4.8. 195- Fixed a compiler error when support for SSSE3 was enabled without support for SSE4.1. 196- Implemented asynchronous loading of seed hits. 197 198[0.9.33] 199- Improved performance and sensitivity. 200- Increased use of temporary disk space. 201- Implemented support for the AVX2 instruction set. 202- Fixed a bug on big-endian architectures. 203- Fixed bugs for compilers with unsigned char. 204- Fixed compiler errors for generic builds. 205- Added compatibility of database files between little and big endian architectures. 206- Fixed various issues related to `Illegal instruction` errors on macOS. 207- Added option `--file-buffer-size` to set the size of the I/O buffers and set the default value to 64 MB. 208 209[0.9.32] 210- Fixed a bug that would generate an incorrect count of positive scoring letters in all output formats. 211- Fixed a compiler error on macOS. 212- Fixed an `illegal instruction` error on macOS. 213 214[0.9.31] 215- Improved performance. 216- Composition based statistics use integer scoring. 217- Option `--quiet` will suppress startup message. 218- Added output field `scovhsp` to print the subject coverage per HSP to the tabular format. 219- Added option `--culling-overlap` to set the minimum overlap with a higher scoring hit for a hit to be deleted and changed the 220 default value from 90% to 50%. 221- Added command `diamond test` to run a series of regression tests. 222- Fixed an off-by-one error of the query end position in the XML output format. 223- (Update 2020/06/08) Due to a bug, since this version DAA files are not backward compatible with previous versions when using frameshift alignment (option `-F`). 224 225[0.9.30] 226- Added support for output field `cigar` to the tabular format. 227- Changed the maximum repeat period to 50 for tantan masking. 228- Changed the tantan masking to ungapped mode. 229- Improved the performance of repeat masking. 230- Added output fields sskingdoms, skingdoms, and sphylums to print subject super kingdoms, subject kingdoms, and subject phylums. 231 232[0.9.29] 233- Fixed a bug that could cause taxonomy features to function incorrectly for databases created by versions 0.9.27 and 0.9.28. 234 235[0.9.28] 236- Fixed a bug that could cause alignment score overflows for scores > 65535 in frameshift alignment mode. 237- Fixed a clang compiler error. 238 239[0.9.27] 240- Improved performance of the seed matching stage. 241- Seed frequency counts are computed based on hit seeds. 242- Added option `--taxon-exclude` to exclude list of taxon ids from search. 243- Compiling from source will no longer perform a native build. Instead, a portable binary that contains code paths 244 for multiple architectures will be produced, with dispatch logic that is invoked at runtime. 245 246[0.9.26] 247- Fixed a bug that could cause undefined behaviour when using a database file of format version < 2. 248- Fixed a compiler error when compiled as generic C++. 249- Program will no longer terminate with an error if unlink system call fails. 250- Added option `--tantan-minMaskProb` to set minimum repeat probability for tantan masking and changed the default value to 0.9. 251- Added option `--tantan-maxRepeatOffset` to set maximum tandem repeat period to consider and changed the default value to 15. 252- Added option `--tantan-ungapped` to use tantan in ungapped mode and changed the default to gapped mode. 253- Changed score matrix lambda calculation for tantan masking. 254- Reference masking is recomputed during alignment runs. 255 256[0.9.25] 257- Added support for the `sscinames` output field to print subject scientific names to the tabular output format. 258- Fixed a compiler error for GCC 8.2. 259- Added option `--stop-match-score` to set the match score of stop codons. 260- Fixed a bug that caused the `qqual` output field to not be correctly clipped to the aligned part of the query. 261- Added output fields `qseq_gapped` and `sseq_gapped` to the tabular format. 262- Raised compiler requirement to GCC 4.8. 263- Fixed a bug that caused the final sequence positions to not be printed in the pairwise format. 264- Allow using `--min-score` instead of `--top` for the LCA computation of the taxonomy output format. 265- Reduced the number of temporary files. 266- Added output field `qstrand` to the tabular format. 267- Database format version changed to 3. 268- Fixed a bug in the `--range-culling` mode that could cause undefined behaviour. 269 270[0.9.24] 271- Fixed a compiler error on macOS. 272- Added --header option to output header for tabular output format. 273- The quality string output in tabular format (qqual field) is clipped to the aligned part of the query. 274- Print '*' as quality string if quality values are not available in tabular output format. 275- Added field 'full_qqual' to print unclipped query quality values to the tabular format. 276- Added field 'full_qseq' to print unclipped query sequence to the tabular format. 277- Added support for using the hyphen character '-' to denote the standard input for input file parameters. 278- Status messages are written to stderr. 279- Fixed a bug that could incorrectly report queries as unaligned in the output of the --un option. 280- Added option '--al' to write aligned queries to file. 281- Added options '--alfmt' and '--unfmt' to set the format of the aligned/unaligned query file (supported values: fasta, fastq). 282 283[0.9.23] 284- Fixed an issue that could cause too high memory usage. 285- Added output field 'qqual' to print query FASTQ quality values to the tabular format. 286- Changed license to GPL. 287- Raised compiler requirement to GCC 4.6. 288- Added option to use the DAA output format for diamond view. 289- Added support for using a FASTA file as the --db parameter in alignment workflows. 290- Added CL (command line) and VN (version) fields to the @PG SAM format header line. 291- Fixed a performance issue for very long query sequences. 292- Added shortcut --long-reads for --range-culling --top 10 -F 15. 293 294[0.9.22] 295- Added output field full_sseq to tabular output format. 296- Database sequences that exceed the maximum accession length will no longer cause an error. 297- Added support for PAF output format. 298- Optimized performance of database taxonomy filtering. 299 300[0.9.21] 301- Fixed compiler errors on some systems. 302 303[0.9.20] 304- Added Bioconda installation instructions to manual. 305- Added official docker release: https://hub.docker.com/r/buchfink/diamond/ 306- Fixed a bug that could cause corrupted output if compression was activated. 307- Fixed an issue that could cause high memory usage by automatic use of the query-indexed algorithm. 308 309[0.9.19] 310- Fixed a bug in the --un function to write unaligned reads. 311- Fixed an issue in the LCA algorithm that could cause an assignment to a higher node. 312- --taxonmap and --taxonnodes parameters now apply exclusively to the makedb command. 313- Added option --taxonlist to filter searches by subject taxonomic id. 314- Changed database format; rebuilding is required. 315 316[0.9.18] 317- Optimized output writing performance. 318- Fixed a bug in the XML output format. 319 320[0.9.17] 321- Fixed a compiler error on FreeBSD. 322- Added option --range-culling. 323- Fixed escape sequences in XML output. 324 325[0.9.16] 326- Fixed a bug that caused an error for non-SSSE3 builds. 327 328[0.9.15] 329- Improved performance of frameshift alignment mode. 330 331[0.9.14] 332- Added support for frameshift alignments. 333 334[0.9.13] 335- Fixed query positions in pairwise format for translated searches. 336- Changed default behaviour of --max-hsps option to report unlimited number of HSPs. 337 338[0.9.12] 339- Fixed dbinfo command to be able to read older database formats. 340- Adjusted XML format for better compatibility with Blast2Go. 341- Fixed a potential error when running multiple instances of Diamond. 342 343[0.9.11] 344- Added option --xml-blord-format for alternative-style XML format. 345- Fixed a bug that could cause a crash when writing compressed output files. 346 347[0.9.10] 348- added --strand option to choose query strand 349- added dbinfo command 350 351[0.9.9] 352- Added taxonomic classification format. 353- Fixed a bug in getseq printing masked residues. 354- Fixed parsing of UniRef100_ sequence id prefixes. 355- Added support for using the staxids output field in diamond view. 356 357[0.9.8] 358- Fixed a compiler error. 359 360[0.9.7] 361- Fixed compiler errors. 362- Changed XML format to print accessions in the Hit_id and Hit_accession fields. 363 364[0.9.6] 365- Fixed compiler errors. 366 367[0.9.5] 368- Added support for named pipes. 369- Added support for reading input files from stdin. 370- Added more elaborate file I/O error messages. 371 372[0.9.4] 373- Improved performance. 374- Fixed a bug in the query-indexed algorithm. 375- Empty sequences are ignored instead of generating an error. 376 377[0.9.3] 378- Fixed a bug that could cause hanging. 379- Fixed a bug that could cause an error when using the staxids output field and the --unal option. 380 381[0.9.2] 382- Fixed a compiler error. 383- Improved performance for very small query files. 384 385[0.9.1] 386- fixed a performance issue 387 388[0.9.0] 389- improved performance 390- improved support for alignments with long gaps 391- removed SEG masking 392- added low complexity masking using tantan 393- changed license to AGPL 394 395[0.8.38] 396- fixed std::exception error messages 397- fixed sequence titles in XML format 398- XML and pairwise format contain full length titles by default 399 400[0.8.37] 401- fixed a bug that would cause an error message for empty DAA files 402- all scoring matrices use the respective default gap penalties from BLAST 403- added check for SSSE3 instruction set 404- added diamond-sse2 to the binary package 405- added staxids field to the tabular format 406 407[0.8.36] 408- fixed a compiler error 409 410[0.8.35] 411- added a check to detect incomplete database files 412- database files will be deleted in case database building fails 413- fixed a compiler error on 32 bit systems 414 415[0.8.34] 416- fixed a compiler error 417 418[0.8.33] 419- modified option --no-self-hits to also require matching sequence titles for filtering of a self hit 420- fixed a bug that could cause a crash in the `joining output blocks` stage 421 422[0.8.32] 423- improved speed and sensitivity 424- fixed an issue that could cause too high memory usage in certain cases 425 426[0.8.31] 427- renamed option --run-len to --min-orf 428- added compositional score adjustments (option --comp-based-stats (0,1), enabled by default) 429- removed --single-domain option and replaced by --max-hsps 430- added option --no-self-hits 431 432[0.8.30] 433- slightly improved sensitivity 434- added option to report unaligned queries (--unal) 435- pairwise, XML and SAM format will report unaligned queries by default 436- added option to filter alignments by subject cover (--subject-cover) 437 438[0.8.29] 439- fixed an issue that could cause a crash when using view on incomplete DAA files 440 441[0.8.28] 442- slightly improved sensitivity 443- added support for the BLAST pairwise format (option -f 0) 444 445[0.8.27] 446- added support for gzip compressed files containing multiple gzip streams 447 448[0.8.26] 449- fixed a compiler error 450- now compiles as generic C++ code without SSE being available 451- added option to write unaligned queries to file (--un) 452 453[0.8.25] 454- fixed a bug with the qseq field in the blast tabular format 455- added qtitle and btop fields to the blast tabular format 456- fixed a bug that could cause a crash when passing a nonexistant input file 457- fixed an issue that could cause unexpectedly long runtimes in certain cases 458 459[0.8.24] 460- error messages when reading sequence files include line numbers 461 462[0.8.23] 463- added option to change the genetic code used for translation in blastx mode 464 465[0.8.22] 466- the Hit_id and Hit_accession fields are now filled for the BLAST XML format 467 468[0.8.21] 469- fixed an error of 'diamond view' when using a custom scoring matrix 470 471[0.8.20] 472- added support for customizing the BLAST tabular output format 473 474[0.8.19] 475- ungapped xdrop score and ungapped and gapped filter scores are now set in bits 476- added support for custom scoring matrices 477 478[0.8.18] 479- fixed a crash bug 480- implemented getseq command to retrieve sequences from database files 481 482[0.8.17] 483- slightly improved sensitivity of fast and sensitive mode 484- added new alignment mode (option --more-sensitive) 485- the scoring matrix parameter will accept upper case spelling 486 487[0.8.16] 488- optimized performance 489 490[0.8.15] 491- fixed a compiler error on Mac 492- fixed a crash on some systems 493 494[0.8.14] 495- fixed a memory leak 496 497[0.8.13] 498- fixed a compiler error for GCC 4.1 and 4.2 499 500[0.8.12] 501- changed database format 502- block size parameter is set only for the alignment commands 503- the program will accept databases created by later versions if the format is compatible 504- improved sensitivity of sensitive mode with some loss in performance 505 506[0.8.11] 507- fixed a compiler error 508 509[0.8.10] 510- added option to directly generate all output formats 511- fixed some GCC 6.1 compiler errors 512 513[0.8.9] 514- optimized performance 515- improved local alignment accuracy 516- fixed some fields in the XML format 517 518[0.8.8] 519- fixed a clang compiler error 520 521[0.8.7] 522- added support for BLAST XML format 523- fixed the gzip compressed output option 524 525[0.8.6] 526- fixed a problem of the Windows version that could cause errors for larger files 527- optimized performance 528 529[0.8.5] 530- optimized performance 531 532[0.8.4] 533- fixed a problem that could cause very long runtimes for highly repetitive sequences 534- optimized performance 535- fixed a bug that could cause too high memory usage in blastp mode 536 537[0.8.3] 538- fixed a problem that could sometimes cause alignments to be missed 539- suppressed reporting of alignments that are enveloped by better alignments 540 541[0.8.2] 542- use parameter -k0 to report unlimited number of alignments 543- fixed a crash bug on Mac OS X 544- fixed a crash when view was used with terminal output 545 546[0.8.1] 547- added option to disable auto appending of DAA and DMND file extensions (--no-auto-append) 548- fixed some compiler errors for GCC 4.6 549 550[0.8.0] 551- fixed a bug that would sometimes cause alignments to be missed 552- fixed a bug that would cause alignments on the reverse strand to be missed in blastx mode 553- temporary directory now defaults to output directory 554- removed dependency on Boost 555- fixed a bug that would cause stop codons to be translated into 'X' 556 557[0.7.12] 558- fixed header string in SAM output to correctly identify the blastp alignment mode 559- added option to filter alignments for a given query cover (option --query-cover) 560- added option to print full subject titles in output files (option --salltitles) 561 562[0.7.11] 563- added --version switch 564- added static build option for CMake build 565- fixed a bug that would cause a return code of 1 without an error 566 567[0.7.10] 568- --log option works on OS X 569- added option to set effective database size (--dbsize) 570- added CMake build option 571- fixed a Clang compiler warning 572- dash characters (-) are ignored (treated as X) in protein sequences 573 574[0.7.9] 575- added --single-domain option 576- fixed a bug that could cause the program not to use all available threads 577- optimized performance 578 579[0.7.8] 580- fixed a bug that could produce an incorrect sort order of HSPs 581 582[0.7.7] 583- fixed a number formatting error in the SAM output format 584 585[0.7.6] 586- fixed a formatting error in CIGAR strings 587 588[0.7.5] 589- fixed a compiler error for Clang 590- compiles on OS X 591- fixed a bug that would not produce the correct sort order for HSPs with e-value 0 592- option --run-len defaults to 1 for sequences shorter than 30 letters 593 594[0.7.4] 595- removed OpenMP dependency 596- using explicit Makefile instead of autoconf 597- file extensions can be named explicitly for DAA and database files 598- HSPs are grouped by target sequence 599- fixed a bug that could produce incorrect output for view 600- fixed a bug that could report an incorrect number of alignments 601- fixed a compiler error for GCC 4.1.2 602 603[0.7.3] 604- changed database format (makedb required) 605- optimized multithreading load balancing 606- removed a non-determinism in alignment computation 607- IUPAC nucleotide ambiguity codes in DNA sequences are accepted and converted into N's 608- SEG masking is disabled by default for blastp mode 609- fixed a memory leak 610- reduced database file sizes 611 612[0.7.2] 613- fixed a bug that could create invalid DAA files when using the --id option 614- added integrity check of DAA files to view command 615- fixed a bug that could cause segmentation fault or file seek errors 616 617[0.7.1] 618- fixed a race condition for opening temporary files 619- temporary files are deleted on ungraceful termination of the program 620- blank lines in FASTA files are tolerated 621- fixed a compiler error for GCC 4.4.7 622- view command can write to standard output 623 624[0.7.0] 625- introduced DAA format 626- reduced usage of temporary disk space and memory 627- fixed a compiler error for GCC 4.1.2 628- fixed a bug that could cause the program to hang when running out of temporary space or memory 629- added --forwardonly option to view command