PretextView v1.0.7

New:

• Debug Report feature that brings backend terminal logs into a report for easier troubleshooting and issue sharing.

Bug fixes:

• Resolved an issue where gridlines could disappear during use.

PretextView v1.0.6

PretextView 1.0.6 — Release notes

Added

Highlight → clipboard (Edit mode)

• **P** in Edit mode copies the current highlighted map range to the system clipboard as human-readable text: for each map fragment in the selection, the original contig name and a local span in megabases along that fragment (per-fragment coordinates, not a single genome-wide position).
• If nothing is actively selected, the copy uses the current edit cursor range.
• A short on-screen “Copied to clipboard” confirmation is shown.
• If the Clipboard Editor window is open, the same text is appended to its buffer (with newline separation between copies).

Clipboard Editor (main GUI)

• **Clipboard Editor** button opens a large text area for notes and pasted content.
• Save as opens a file dialog to write the buffer to disk (default filename suffix **_clipboard.txt**).
• Standard shortcuts: Ctrl+C / Ctrl+V / Ctrl+X (Windows/Linux) and Cmd+C / Cmd+V / Cmd+X (macOS), using the system clipboard via GLFW.

Input handling for Nuklear text fields

• **NK_KEYSTATE_BASED_INPUT** is enabled so polled GLFW key state matches Nuklear’s expectations (correct press vs hold behaviour).
• While the main GUI is open, Delete, Enter, Tab, Backspace, arrow keys, Shift, and Ctrl/Cmd+C/V/X are forwarded to Nuklear so the Clipboard Editor and other text widgets behave like typical desktop fields.

---

Fixed

Copy-to-clipboard coordinates

• Clipboard text previously scaled **contigRelCoords** by the global bp-per-pixel factor (Total_Genome_Length / Number_of_Pixels_1D) as if they were genome-wide indices. That mixed local fragment indices with a global scale.
• Copy now uses each fragment’s **startCoord**, **IsContigInverted**, and the same uniform map resolution so reported Mbp ranges are local along each fragment (aligned with map state).

Clipboard Editor usability

• Cut/copy/paste and basic editing keys now reach Nuklear when the UI is active (state-based input + explicit shortcut forwarding).

Pixel Sort / “select sort area” (fragment sort)

• Local → global order mapping when sorting only a selected region was wrong (it anchored indices on the first selected fragment). The sorter’s local signed order is now mapped to the correct global contig ids via frags_id_to_sort[local_index − 1].
• **UpdateContigsFromMapState()** is run after copying textures / restoring colour before auto-sort so **contigIds** matches the on-screen map (rearrange updates other buffers first).
• Selection bounds: pixel indices must satisfy **0 ≤ start/end < number_of_pixels_1D** so the code never indexes past the end of **contigIds**.
• Noisy contig ids at fragment boundaries (single-pixel flips) are smoothed (median-of-3) and long alternating A/B runs are collapsed, so select-area sort does not build huge duplicate fragment lists.
• Source / sink neighbours for clustering are computed reliably: state is cleared each time, and left/right neighbours use correct bounds (including “no neighbour” at the map ends).
• Compressed Hi‑C / zero-length contigs: empty blocks no longer assert; **cal_block_mean** and related paths skip or return safe values; warnings when a contig has length 0.

Edit mode: contig pickup / multi-select (mouse & space)

• Middle-button or space release no longer toggles “pick up / place” (Edit_Pixels.editing) unless you were actually in multi-select mode (Edit_Pixels.selecting). Previously, releasing middle or space while not editing could still flip into editing as if a pickup had completed, which was wrong outside a multi-selection gesture. Clearing selection and entering place mode now happens only when finishing a real multi-select (pickup_contig fix).

PretextView v1.0.5

Main Changes
Core Functionality:

1. Pixel Sort Bug Fixes: Critical fixes to sorting algorithm, improved stability and link score calculation
2. Savable Edit Feature: Tracked Edits can now be saved to text file.

UI Enhancements:

1. Global 3 and 5' Telomere Shortcuts: Keys 3 and 5 work globally
2. Universal Search Box added to Save/Load State and Generate/Load AGP dialogs
3. Top level menu keybinding change -> [ESC]

PretextView - 1.0.4

Main changes:

• Cluster before sorting. Usage: decrease or increase the number of clusters by pressing left or right SHIFT key. (no clustering while number of cluster is one).
• Raised the maximum numbe of contigs to 16384 to avoid overflow problem. (Note: We use the remainder for segmentation. For example, 0 and 16384+0 belong to the same original contig. However, they are segmented into different fragments. Similarly, 10 and 16384+10 also belong to the same original contig, but are segmented into different fragments. Thus if the orignal number of contigs is larger than 16384, it will be treated as the same original contig but defferent fragments.)
• Fixed some bugs.

PretextView - 1.0.3

Name the Sort and Cut functions as Pixel Sort and Pixel Cut.

Main changes:

• changed to use key F to toggle select sort area mode.
• added Pixel Cut function, which can be used in global mode (by left clicking button in main menu) or select sort area mode.
  • the pixel discontinuity is calculated and pushed to extensions automatically while loading the .pretext file
  • the Pixel Cut is implemented by adding 4096(max number of contigs) to the original_contig_id.
  • sensitivity can be adjusted by setting the cut threshold in the Pixel Cut setting window, which can be opened by right click the Pixel Cut button in main menu.
  • add up/down arrow key under select sort area mode to increase / decrease the cut threshold.
• modified the local sort function:
  • fixed the two ends while sorting locally
  • add left/right arrow key under select sort area mode to switch the sorting algorithom.
• added Select Active Tag in the main menu to select the active meta tag to label the fragments.
• added Grey Out Tags to select the tags to be coved with grey mask.
• fixed bug of copying high resolution contact matrix buffer to cpu: used to make the sort and cut function doesn't work withi high resolution samples.
• optimized the link score calculation:
  • modifying the weight vector from linear to non-linear;
  • add extra 5 pixels length to the weight vector to make the link scores lower for fragments with short length. The shorter the weight is relatively lower.
• added color blind color map.
• added the color settings for selected area in user profile.
• move invert mouse setting to user profile.

PretextView 1.0.1 (Three platforms supported)

• Windows-x86_64, Linux-x86_64, Mac-x86_64, and Mac-arm64 are supported.
• Fixed path error for shader source files.
• Fixed crash down problem for Windows while using YAHS sort. This error is caused by the uninlitilised pointers within the object in the fragment sort source code.
• Fixed torch lib error for Linux, currently the AI model is excluded from this release. In the future we are going to introduce the AI module inside, which will include the torch library again.
• Add deploy.yml which will automatically run and upload the install packages to the release page. This deploy action will start when new tag is created.

NOTE for Mac user who downloads this from Release page. If the user is told that the software is damaged, please eject the mounted dmg file and run

xattr -d com.apple.quarantine /path/to/the/downloaded/dmg/file

to remove the quarantine and re-mount the dmg file. And then try to open the PretextViewAI.app.

PretextView 1.0.0

What's Changed

Features added:

• Automatic curation: YaHS algorithm sorting of contigs, globally or locally within selected area

• UserProfile function: background color, color map, meta tag style, extension graph style

• Input sequence search and adaptive zoom locating

• Jump to diagonal after fragment selection whilst in edit mode

• Change to waypoints - vertical, horizontal, cross

• Embedded extension track toggle menu (x)

• Top level extension track toggle for "coverage" and "gap"

• Updated Metadata tags list

• Metadata tags sorting function

• Map cache clear function

• Compile script is changed from meson to CMake

• Icon updates to new version v1.0.0

New Contributors

• @guanshaoheng
• @atharvfakatkar

Full Changelog: 0.2.5...1.0.0

PretextView 0.2.5

0.2.5 full release

Full Changelog: 0.2.4...0.2.5

PretextView 0.2.5 devel release 2

0.2.5 development release version 2. Shouldn't be considered production ready.

New features:

• Option to preserve sequence order in AGP output.
• Option to display embedded graph labels.

Note: Save-states only compatible with previous version (0.2.5-dev-1).

Full Changelog: 0.2.4...0.2.5-dev-2

PretextView 0.2.5 devel release 1

0.2.5 development release version 1. Shouldn't be considered production ready.

New features:

• More default tags
• Painted sequences auto-tagged in AGP output
• Higher resolution support (experimental)

Note: Save-states not compatible with previous version.