Chromonomer 1.15 - October 8, 2024 ---------------------------------- Bugfix: when employing the --rescaffold option, some markers that were removed because they were in conflict with the order of other markers, were not removed from the internal scaffold representation of the assembly. This could lead to a segfault when the program tried to later access these removed markers when examining scaffolds. Feature: the translate_gtf.py and fasta2agp.py scripts were updated to Python 3. Chromonomer 1.14 - July 14, 2022 -------------------------------- Bugfix: some scripts that create AGP files from FASTA files set the starting basepair of the scaffold object in the second column to "0" instead of "1" (e.g. makeAgpFromFasta.py from JuiceBox). This implies the scaffold starts at 0, which could result in a segfault in chromonomer when it tried to translate the FASTA file after integration. The AGP standard (https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/) states that the starting basepair columns should be 1-based, not 0-based. We added a check and error message when parsing the AGP to prevent the segfault. Feature: converted Python scripts to Python 3. Chromonomer 1.13 - October 23, 2020 ----------------------------------- Bugfix: For rescaffold option, some markers that overlap in position on a scaffold were not being pruned properly, leading to a segfault. Bugfix: If using conserved synteny information to order scaffolds, if no valid orthologs were available for the analysis a segfault could occur. Chromonomer 1.12 - September 3, 2020 ------------------------------------ Updated package to include newer Python scripts including fasta2agp.py and translate_gtf.py Chromonomer 1.11 - May 28, 2020 ------------------------------- Feature: Added a utility script, fasta2agp.py, to extract an AGP file given an assembly FASTA file. Feature: chromonomer now produces a 'promising scaffolds' list. This is a list of scaffolds with markers mapped to them that are not included in the linkage map. If some of these markers could be added to the map, the corresponding scaffold could be chromonomed. Bugfix: when parsing the linkage map definition file, there was a missing error check to make sure the cM position was read properly. If the file contained Windows line endings ("\r\n") it resulted in all of the cM positions erroneously being -1. Added error check and code to handle "\r\n" line endings. Chromonomer 1.10 - February 6, 2020 ----------------------------------- Feature: Added 'virtual break points' (--depth option). Using read alignments, chromonomer can now infer breakpoints based on read coverage (by calculating variation from mean read coverage along the assembly). This allows a method to split missassembled scaffolds from long-read assemblies (that do not otherwisehave gaps). Feature: Added 'rescaffold' option, which allows the genetic map to break contiguous regions of an assembly (no scaffolding gaps present). Useful for gapless, long-read assemblies. Often combined with the virtual break points option. Feature: Added conserved synteny options. Specifying --gtf, --orth_gtf, and --orthologs, gene synteny from a nearby genome can be used to order/orient if they are not ordered directly by the linkage map (Adds information to unordered parts of the linkage map, does not override the linkage map order). Chromonomer 1.09 - June 5, 2019 ------------------------------- Bugfix: Updated SAM parsing code to handle aligned sequences longer than 1024bp. Feature: Updated to HTSLib 1.9. Bugfix: Scaffold-level AGP file was missing a column in some cases. 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.