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.
π Walkthroughπ Walkthrough
## Walkthrough
The pull request introduces modifications to two files: `build.sh` and `meta.yaml` within the `PretextGraph` package. In `build.sh`, the C++ compiler setting has been updated from `clang` to `clang++` for non-Darwin systems, ensuring the correct compiler is used for C++ files while maintaining the overall structure of the script. In `meta.yaml`, the version number is incremented from "0.0.6" to "0.0.7". The source URL has been altered to point to a new repository, changing from a previous GitHub URL to a new one with a `.tar.gz` file format. The SHA256 checksum has been updated, and the build number has been reset to 0. Additionally, a new field `run_exports` has been introduced under the build section, specifying a dependency on the `pretextgraph` subpackage with a maximum pinning of "x.x". The requirements section remains largely unchanged, with only formatting adjustments to the spacing of the `clang` and `meson` dependencies.
## Suggested labels
`autobump`, `new version`
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π₯ Commits
Files that changed from the base of the PR and between 17bee969ac5f4d711b8a6884540a87bc65f0a0df and 55cbecd0dae70780626b82084cae700b1f06bdfc.
π Files selected for processing (1)
* recipes/pretextgraph/meta.yaml (1 hunks)
π§ Files skipped from review as they are similar to previous changes (1)
* recipes/pretextgraph/meta.yaml
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Update PretextGraph to 0.0.7
Fixes and Improvements:
graph->values
by changing the calculation type from u32 to f32.data_type
for handling different methods of transforming thebedgraph
file intoGraph->values
:gap
: Sets the pixel value with numberindex
forGraph->values[index]
containing the gap to1
.repeat_density
: Normalizes the value of each bin as a percentage, reflecting the ratio of repeat pairs within that bin. For instance, if thebin_size=10,000
andN
base pairs are marked as repeats, the ratio is calculated asN / 10,000
.default
: Retains the original calculation method.PrintStatus
: Resolved small bugs that caused the program to crash.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 foru32
. Currently, it will be set as 0.