Release 0.4 (08 July, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Bug fixes:
 * Correct SAM output in case of long reads (longer to 500nt)
 * Aligning a simple hit: remove case of infinite loop 
 * Correct computation of qpalma score for unspliced alignment
 * Correction of soft clipping position in CIGAR string and start position of read according to a presence or soft clipping at the beginning of the read
 * Quality offset of 64 instead of 65 for phred64
 * All cases of unmapped reads are now reported in the unmapped read file or the sam file (option -include-unmapped-read)

Non-consensus search option:
This option enables PALMapper to output spliced alignments whose
splice sites are not within the known consensus sequences. These
alignments are provided only if they do not overlap another spliced 
alignment with consensus splice sites.  

Remapping strategy:
 * Report splice junctions from spliced alignments
 * Map reads with the classical strategy or against the splice junctions found from a previous mapping or from the annotation

Annotated splice sites (-score-annotated-splice-sites option):
 * Score to 1 annotated acceptor and donor sites
 * Use annotated splice sites for building the pseudo chromosome sequence
 * Use annotated splice sites for filtering reads which need a spliced alignment

Other notable changes:
* Add -include-unmapped-reads option. This option outputs unmapped
reads in the same file than mapped reads (valid only for sam output). 
* Add bam output
* Add -fixtrimleft and -fixtrimright options to trim the beginning or the end of each
read by a given number of nucleotides before processing.
* Add -protocol <first|second> option to take into account strand-specific protocol (non strand specific by default)

(0.4: 08 July 2011, r23380)

Release Candidate 0.4-rc4 (02 February, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release introduces a lot of changes since the last version and
fixes a few bugs. The documentation of PALMapper is now available in
PDF format under the subdirectory doc/. Please, consult the
documentation for more information about how to use this software.

Notable changes in palmapper output:
 * Fixed bugs which may lead to incorrect cigar string or incorrect
 exon length in SAM file
 * Add more informative tags in SAM output: ZS, Xe, Xi, XI, XN, HI,
 AS, XQ, XD, Xd. Consult the documentation for more information
 * Give strand flag only for splice reads
 * Fixed bug for minimal exon length in Bedx output

Notable changes in palmapper options:
 * add -acc-consensus and -don-consensus options to define splice site 
 consensus sequences to consider (options have to be jointly used with
 -no-ss-pred)
 * Add -non-consensus-search option (search for a spliced alignment
 with non consensus splice sites which does not overlap with a spliced
 alignment with known consensus splice sites)

Other notable changes:
 * Multithreading
 * Allow seed lengths up to 15 for array-based indexes
 * Genome coverage computation (-report-coverage-wig option)
 * Add fast mapping with bwt-based index (Burrows-Wheeler
 Transform). We use the sources from BWA (Burrows-Wheeler Alignment
 tool) which are located under src/bwa. The use of bwt-based index
 should give the same results than with the use of the array-based
 index provided by GenomeMapper. This version is experimental.
 * New QPALMA pretrained models (for small and large genomes and short
 and long reads without splice site predictions).
 * More testcases to test different options.
 * Remove MAX_EXON_LEN variable which could lead to aborted execution
 for long reads

(0.4-rc4: 02 February 2011, r21526)


Release Candidate 0.4-rc3 (09 May, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in palmapper:
 * Improve rtrim and polytrim strategies
 * Set SAM as default output format for mapped reads
 * Set /dev/null as default output file for unmapped reads
 * Merge unspliced and spliced alignments in the same output if -H
 option not given
 * Save space by using smaller index (don't generate index for negative strand)
 * add -no-ss-pred option to compute alignments without using splice site predictions

(0.4-rc3: 09 May 2010, r18597)


Release Candidate 0.4-rc2 (19 April, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in palmapper:
 * Improve BED output for rtim strategy
 * Global change from genomemapper to palmapper (in src directory)
 
Notable changes in pmindex: 
 * Global change from mkindex to pmindex (in src directory)

(0.4-rc2: 19 April 2010, r18207)


Release Candidate 0.4-rc1 (16 April, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is the first release of the alignment tool PALMapper, which is
the fusion of QPALMA and PALMapper. Please consult the webpage
http://www.fml.tuebingen.mpg.de/raetsch/suppl/palmapper/ for more
information about this software.   

(0.4-rc1: 16 April 2010, r18141)