PretextGraph-0.0.9

Changes:

• removed the normalisation for repeat_density extension. The repeat density was normalised by the bin_size. But there are some bins with different sizes, which will make the repeat_density signal incorrect.
• removed the dependency of Wrapper by adding the SIMDExtensionWrapper.cpp inside of the project.
• change the function of stbsp_snprintf to snprintf to avoid segfault.
• update version number to 0.0.9

PretextGraph-0.0.8

• Fixed the problem of gradually dropping to 0;
• Added noise_filter to coverage and repeat_density to avoid the extension is visually like a line due to the extra high noises.
• Updated the extension data types.

Fixed bugs

Fixes and Improvements:

• Resolved the gap extension issue:
  • Addressed data overflow when calculating graph->values by changing the calculation type from u32 to f32.
  • Introduced a new data_type for handling different methods of transforming the bedgraph file into Graph->values:
    • gap: Sets the pixel value with number index for Graph->values[index] containing the gap to 1.
• repeat_density: Normalizes the value of each bin as a percentage, reflecting the ratio of repeat pairs within that bin. For instance, if the bin_size=10,000 and N base pairs are marked as repeats, the ratio is calculated as N / 10,000.
• default: Retains the original calculation method.
• Fixed a segmentation fault in PrintStatus: Resolved small bugs that caused the program to crash.
• Improved ProcessLine function: Added a check to ensure (u32) nThisBin does not become negative. Originally, if a negative value is encountered, it will be set to the maximum allowable value for u32. Currently, it will be set as 0.
• Compilation adjustments: Since modifications were made in C++, the compiler has been switched to Clang++ to resolve compilation issues.

PretextGraph-0.0.6

0.0.6

PretextGraph-0.0.5

Auto-generated release by Travis CI

PretextGraph-0.0.4

Auto-generated release by Travis CI

PretextGraph 0.0.2

updated readme