Chromonomer 1.08 - May 21, 2018 ------------------------------- Feature: Changed internal representation of Markers so that marker IDs are strings, rather than integers. Feature: Updated HTSLib to 1.7. Bugfix: cleaned up code, updating it to newer C++ conventions. Chromonomer 1.07 - Aug 13, 2017 ------------------------------- Feature: Added support for BAM files and gzipped FASTA, AGP, and linkage map files. Bugfix: Fixed bug that occurred when too many decimal places were used when specifying centiMorgan nodes in the genetic map. In these cases, the nodes could be rounded casusing nodes to improperly collapse together. Bugfix: the use of unsigned ints in the summary function could result in genome sizes with negative values due to the values being too large for a uint and causing that variable to wrap around into negative space. Chromonomer 1.06 - Oct 13, 2016 ------------------------------- Fixed build issue where C++11 compile flag was not be passed into build process. Chromonomer 1.05 - July 21, 2016 -------------------------------- Feature: scaffold splitting algorithm is now more robust and can partially split a scaffold even when there are some split conflicts within the scaffold. Feature: added checks to identify markers with multiple alignments and to remove markers where multiple markers align to the same genomic position. Feature: added --description option to allow user to supply a description of a particular chromonomer run and have it written into the ouput log file. Feature: added --disable_splitting flag. When provided, chromonomer will not split any scaffolds, it will just place each scaffold in the map where the majority of markers occur. Feature: Chromonomer will now write the final linkage map (having pruned markers from it) back out to disk. This can be used for visualization in Synolog, or as a base to update a map in linkage mapping software. Chromonomer 1.04 - June 24, 2016 -------------------------------- Feature: added the --join_gap_size parameter to control the size of gaps inserted between joined scaffolds. Bugfix: fixed a logging problem where if you split the scaffold between LGs, and then split it again within an LG, you would overwrite the first half of the log when starting the second. Bugfix: improved FASTA parser to handle comments embedded in FASTA ID line and to handle sequences written without any line breaks. Chromonomer 1.03 - January 29, 2016 ----------------------------------- Feature: Added FASTA export; if provided a FASTA file of the assembly this option will translate the sequence according to the chromonomer integration of the assembly and map. Feature: Added tiny test data set in the test/ subdirectory. Bugfix: Chromonomer was propogating orientation information for some scaffolds that was no longer valid after a scaffold split. Chromonomer 1.02 - Dec 23, 2015 ------------------------------- Feature: Added SVG visualization of before/after chromonomer assembly integrations. Feature: Added JSON formatted export of map/assembly integration. Chromonomer 1.01 - Dec 09, 2015 ------------------------------- Bugfix: Completed new hueristic code to remove out of order markers. Bugfix: Adjusted scaffold coordinates when more than one break was made. Bugfix: Updates to the web interface. Chromonomer 1.0 - June 03, 2015 ------------------------------- Initial public release of Chromonomer.