SVDetect Files

==== SVDetect release notes =====


* r0.8b - 2013-01-22

New version of the "BAM_preprocessingPairs.pl" script (0.5)
- update regarding the flag bitwise of the "one unmapped read" pairs with the SAM 1.4 specification format

* r0.8 - 2011-12-06

- Parallelized computing in linking, filtering and cnv functions per chromosome
- New perl libraries required : FileHandle - Parallel::ForkManager
- Addition of the "num_threads", "tmp_dir", "split_mate_file", "split_link_file" parameters
- Modified configurations files in the test sample Neuroblastoma

* r0.7m - 2011-07-12

- Change of the parameters location in the config file: read1_length, read2_length, mates_file, cmap_file located in the <general> block
- The <compare> block is now completely independent
- Addition of the list_read_lengths parameter in the compare block (in case of different libraries)
- Modified configurations files in the test sample
- Identification of medium-size duplications for Illumina paired-end/mate-pair data

* r0.7f - 2011-01-10

- The "File::Sort" perl library is not required anymore
- The strand filtering decision has changed, links having two populations of different pair orientations are not discarded but splitted
- The consistency of the sens strand orientation of pairs in the order filtering is now assessed for SOLiD mate-pairs
- Identification of additional SV types according the balanced signatures of consistent mapped pairs
- Identification of singletons (Illumina mate-pairs only), addition of the "singleton_sigma_threshold" parameter
- Clusters with an undefined SV type are not discarded (type is "undefined")
- Addition of the "final_score_threshold" parameter (post-filtering process)
- The "links2compare" function requires BEDTools, addition of "min_overlap" and "same_sv_type" parameters
- Modified configurations files in the test sample
- New version of the "BAM_preprocessingPairs.pl" script (v0.4), lower and upper limits of ISIZE can be set for a better calculation of mu and sigma lengths 
- README update (v1.10)

* r0.6d - 2010-09-10

-Sorting and removing fully overlapped links at the end of any filtering step
-Faster compare algorithm
-Few bug fixes

* r0.6c - 2010-08-03

Bug fix in the tabulated file format for *.links.filtered files

New version of the "BAM_preprocessingPairs.pl" script (0.3)
- Bug fixes in the sam file name extension for BAM conversion
- Easy input parameters : Illumina/SOLiD and paired-end/mate-pair boolean values


* r0.6b - 2010-07-26

Addition of the perl script "BAM_preprocessingPairs.pl" located in the
new scripts/ directory.


* r0.6a - 2010-07-21

Addition of new features:
- Use of different read lengths between ends in a pair
(compatibility with SOLiDv4 paired-ends, ex. F3:50bp F5:35bp)
- Output directory option
- BAM file accepted as input format (SAMtools required)
- Faster strand filtering process
- Lower memory usage (>3X)
- Score of the insert size filtering provided
- Start coordinates in link files correspond to sequencing starts
(=first base of reads instead of the leftmost position)
- Best definition of breakpoint starts and ends for SOLiD data

Removed features:
- No filtered mate files created (links only)


* r0.5  - 2010-04-30

First official release of SVDetect