ChangeLog

-- Version history --

(If not otherwise stated, changes apply to the standalone and web version.)

deconseq-0.4.3:
Fixed issue when multiple chunks per database were specified in the config file
that did not correctly split during search. (Thanks to Osvaldo Zagordi for
pointing out the problem.)

deconseq-0.4.2:
Added FindBin module to find config file when run from outside the source
directory. Improve readme file. Allow multiple chunks per database to be
specified in the config file and used with a single database name in -dbs.

deconseq-0.4.1:
Fixed issue with missing method generateFastaFromIds. (Thanks to Valmik Desai
for pointing out the problem.) Extended the input format from ACGTN to full
nucleic acid ambiguity code (ACGTURYKMSWBDHVNX-).

deconseq-0.4:
Added FASTQ support to standalone version.

deconseq-0.3.2:
Fixed issues of undefined output during FASTA file generation and grouping when
using option dbs_retain.

deconseq-0.3.1:
Removed debugging print out (3).

deconseq-0.3:
Updated BWA-SW from 0.5.8 to 0.5.9 (bugfix of very rare mismapping and change of
scoring matrix, see http://bio-bwa.sourceforge.net/ for more details). Allow
FASTQ file format for download (web version). Use input file name with added
string as output file name.

deconseq-0.2:
Code cleanup. Added access to bwasw parameters -S (chunk size of input),
-z (Z-best value) and -T (score threshold). Use -f instead of '>' for output
generation. Modified BWA-SW file bwtsw2_aux.c to allow SAM and alternative
DeconSeq output. Modified BWA-SW files bwtsw2_main.c and bwtsw2.h to fix double
defined params (-s given twice, changed one to -S) and added new parameter -A
for alternative output selection. Changed BWA-SW files stdaln.c, stdaln.h and
bwtsw2_aux.c to include R for replacement in CIGAR strings instead of using M.
Added parameter -R to BWA-SW to output extented CIGAR string instead of standard
version. Modified BWA-SW file bwtsw2_aux.c to always mismatch ambiguous base N
in query sequence instead of randomly replacing it by A, C, G or T. Added
parameter -M to BWA-SW to force always mismatch of Ns in query.
Web version only:
Fixed hash issue while parsing TSV file in process_data.pl file. Fixed issue in
parsing FASTQ files with no information in '+' header line.

deconseq-0.1:
First public release of DeconSeq.