Version 1.41 * Added missing INSTALL.pl script. * Make it clear that this library only works up through Samtools 0.1.19. * Improvements to INSTALL.pl script and documentation. Version 1.40 * Add Bio::DB::Bam::Alinment->qstring() convenience method. * Add reference to GitHub site for this module. * Add -force_refseq option to Bio::DB::Sam->new() constructor to force module to use the FASTA file for reference sequence retrieval even when MD flag is available. Version 1.39 * Bio::DB::Bam::Alinment->strand() performance patch from: https://rt.cpan.org/Ticket/Display.html?id=88203. Version 1.38 * Add -lpthread to linker flags to allow to run with samtools 0.1.19. Version 1.37 * Fix incorrect calculation of mate_len and mate_end when CIGAR string contains insertions and deletions. Thanks to Ian Sealy for the patch! Version 1.36 * Added C binary bam2bedgraph for quick coverage calculations (2-5x faster than BEDTools' genomeCoverageBed) * Speed up bamToGrowse.pl using bam2bedgraph. Version 1.35 * Add patch from John Marshall to fix several problems in the tam line generator when reads are unmapped. Version 1.34 * Add patch from Florian Finkernagel to accomodate paired end data that are encoded as CIGAR strings. Version 1.33 * Fix compile error on perl 5.8.7 and lower. * Fix "substr outside of string" errors when processing split alignments with a hard clip at beginning of CIGAR string. Version 1.32 * Fix loss of strand information when joining split alignments. * Give read_pair objects a primary_id that will allow them to be retrieved intact using get_feature_by_id(). Version 1.31 * Added Bio::DB::Sam->max_pileup_cnt() and Bio::DB::Bam->max_pileup_cnt() method to allow users to adjust Samtools cap on pileup depth. Version 1.30 * Apply patch from Jason Walker to return full arrays across 0-depth coverage and to max the count at a certain coverage. Version 1.29 * Apply patch from Hongwen Qiu to fix memory allocation error in bam header generation. Version 1.28 *Fixed coverage calculations so that sections of reads that cover the reference genome which are marked in the CIGAR string as 'N' (skip) or 'D' (delete) do not contribute to coverage. *The bamToGBrowse.pl script now takes advantage of genomeCoveragetoBed from the BedTools package. If this executable is installed, BigWig generation will speed up noticeably. Version 1.27 *Support for SAM/BAM files in which the sequence is given as "*". This will return a completely ambiguous read (NNNNNNNN) of the proper length. *SamToGBrowse functions will now work properly under a fastCGI environment. Version 1.26 * Added support for samtools >= 0.1.9 is_refskip field in pileups. Version 1.25 * Removed debugging warning in get_feature_by_id(). * Identify version-specific samtools installs where the prefix is xyz and the include/lib files are in xyz/include and xyz/lib (Contributed by John Marshall). Version 1.24 * More revisions needed to run tests succssfully. Sorry! Version 1.23 * added missing files needed for the multi-gaps test introduced in 1.22. Version 1.22 * fix/test for 'incomplete cigar/split alignments processing of multi-gaps' (https://sourceforge.net/tracker/?func=detail&aid=3083769&group_id=27707&atid=391291)" Version 1.21 * Fixed the AlignWrapper->can() method, which was causing crashes with GBrowse2. Version 1.20 * Added Bio::DB::Tam->header_read() method. Version 1.19 * Added Bio::DB::Bam::Alignment->mate_seq_id() method. * Added Bio::DB::Bam::Alignment->aux() method. * Added Bio::DB::Bam::Alignment->tam_line() method. * Fixed Bio::DB::Bam::Alignment->cigar_str() method to return fields in correct order! (bad bug) Version 1.18 * Made the BAMfile $header->text() method read/write, allowing limited modification of header fields. * Fixed MD processing again to correctly handle insertions into the reference sequence. Version 1.17 * Fixed bug in processing of MD tag that returned incorrect reference sequence when alignment contains soft clips. * Fixed processing of "A" tags so that they return the appropriate 1 character string rather than undef. Version 1.16 * No longer attempt to build BAM index automatically if the .bai file is either missing or out of date. Pass -autoindex=>1 to Bio::DB::Sam to restore original behavior. Version 1.15 * If -fasta argument is not provided at new() time, methods will attempt to use the MD tags to reconstruct reference sequence. Version 1.14 * A last minute typo broke the regression tests. This is now fixed. Don't use version 1.13. Version 1.13 * Fixed another bug in padded_alignments(), which caused the source dna sequence to be reported incorrectly for mismatches. Thanks to David Gacquer <firstname.lastname@example.org> for identifying all these bugs. Version 1.12 * Fixed the padded_alignments() method to correct "method not found" bug introduced in version 1.11. Version 1.11 * Fixed the padded alignments returned for hard-clipped alignments. Version 1.10 * Added a new Bio::DB::Bam method for caching remote files' indices in the temp directory. This is used by default by high-level API. * Fixed bug in soft and hard clipping code; query endpoints should be correct now. * Fixed bug in get_all_tags() which was choking on "Z" style tags and giving scrambled results. * $feature->query now reports the DNA query in canonical (ref) coordinates; only $feature->target reverse complements the query DNA to give the data actually read; cigar string is always in canonical coordinates Version 1.09 * Disabled checks for file readability when path is a remote BAM index. This allows transparent access to BAM databases on http/ftp servers. Version 1.08 * Implemented a clone() method for use immediately before or after a fork() attempt. Version 1.07 * IMPORTANT API CHANGE 1: The feature strand now returns +1 or -1 to indicate whether the query was reverse complemented in the SAM file. * IMPORTANT API CHANGE 2: The $feature->query object's dna() and seq() methods now return the sequence as it was read, rather than the reverse complemented version as represented in the SAM file. $feature->qseq() returns the reverse complemented version as before. Version 1.06 * Updated README to be more explicit about how to troubleshoot compile errors. * Modifed so that Bio::DB::Sam will work with GBrowse 1. Version 1.05 * Bio::DB::Sam->seq_id() method no longer lower-cases reference names. * Quashed enormous memory leak in the pileup() function. Version 1.04 * Updated example BAM file (ex1.bam) to be compatible with 1.06 version of samtools. Version 1.03 * Fixed documentation on running with GBrowse. * Fixed alignwrapper behavior so that GBrowse searches don't crash. Version 1.02 * Fixed bug in parsing of unsigned integer tags that caused some tags to be treated as signed integer. Version 1.01 * Fixed Build.PL to pick up correct location of bam header files. * Eliminated several memory leaks that manifested when reading BAM files with lots of targets. * Made -fasta argument optional when using high-level interface. Version 1.00 * initial release Tue Jun 23 23:47:28 BST 2009 * Many documentation improvements * Improved performance of high-level interface for fetch() and pileup() functions. * Added information to README about how to compile with samtools 0.1.4 Thu May 7 09:47:02 EDT 2009 * See t/01sam.t for a demonstration of the API. * Essentially all of the API is fleshed out, with the exception of the ability to generate padded alignment itself. * The $alignment->query() interface is the one to use for retrieving start, end and sequence of the query sequence. The $alignment->target() interface flips the meaning of start and end when the alignment is reversed, to accomodate old AceDB/GFF2 scripts.