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CHANGELOG.md

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CHANGELOG

0.4.3

  • Fixed reading and writing empty contact lists.

0.4.2

  • Fixed broken --diploid mode.

0.4.1

  • Added --bead-wells to mflock to add bead-specific attractors.
  • Added --diploid to mflock to explicitly inform that the labels should be duplicated (since diploid structures are generated from a Hi-C matrix which does not differentiate between the two copies).
  • Added some toy examples under /examples
  • Added the color map under /doc

Broken:

  • make SDL=0.

0.4.0

  • Sparse representation of contact restraints Lists of contact pairs, replace the contact indicator matrices previously used. This change does significantly reduce the storage required for a dataset and also reduces the processing times somewhat. On the other hand it breaks compatibility with older versions.

    The overall usage procedure should not be changed though. The typical chain of commands:

    chromflock init
edit chromflock_gen
./chromflock_gen
./chromflock_run

    is the same.

  • Refactoring and commenting: Parts of the code has been refactored to be easier to read and understand. Comments has been added along the way but the source is still far from being fully documented.

makefile:

  • The -fanalyzer flag has been added to the debug builds. Currently no warnings are issued for any of the binaries with GCC 11.4.

aflock:

  • Removed unused command line arguments.
  • Output files have new names and format. afock -F does now produce: assigned_contacts.u16 and measured_contacts.u16.
  • Assigned contacts are stored as contact-pairs.u32.gz in the structure folders.
  • RAM requirements reduced to approximately 1/4 of the previous version due to change of data types.

mflock:

  • Command line arguments changed.
  • Removed the option to set the simulation parameters from command line.
  • Reads/writes gz compressed contact pairs instead of the binary indication matrix (W.uint8).
  • Writes ISO time to log files at start and finish.
  • Writes the command line to the log file.

chromflock string2any/any2string

  • Added uint16_t and uint32_t to the list of supported data types. Also short aliases will work, i.e.: u8, u16, u32.

0.3.9

  • Compiles with -pedantic and -fanalyzer without any warnings with gcc 11.4.0.

0.3.8

  • Fixed issues with the makefile. SDL is used by default.
  • Automatic RAM usage limitation (only on Linux) which should give a more graceful exit than SEGMENTATION FAULT when running out of RAM. The process is quite crude so it might not work in all situations (only checks the amount of free RAM once).

0.3.7

  • Fixed infinite loop when finding scaling factor in hic2cpm (again!).
  • Fixed the --aOut argument which was ignored (hic2cpm).

0.3.6

  • Added the --mean option to chromflock hic2cpm.

0.3.5

  • Fixed issues that hic2cpm sometimes didn't find a scaling value.

0.3.4

  • Cleaned up the makefile
  • mflock.lua is now created by chromflock init, forgot that in the previous version.

0.3.3

  • New behaviour, instead of chromflock, do chromflock init.
  • cc2cpm is baked into the binary chromflock and renamed to hic2cpm
  • sprite2cpm, any2string and string2any also moved to chromflock.
  • documentation is based on markdown instead of troff.

0.3.2

  • Cleaned up the makefile.
  • Added --version argument to aflock, mflock, and cc2cpm
  • Fixed typos in the cc2cpm documentation.

0.3.1

  • Added script to make a deb package for Ubuntu. That is the preferred way to install from now.