Not ready to merge#18

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amkram wants to merge 439 commits intowas-mainfrom

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Commits on Jul 30, 2024

Commits on Aug 1, 2024

Commits on Aug 2, 2024

faster coordindex
AlanAlohaUCSC
committed

Commits on Aug 5, 2024

Commits on Aug 20, 2024

Commits on Aug 26, 2024

Update README.md
amkram
authored

Commits on Aug 28, 2024

Commits on Aug 30, 2024

devoding
amkram
committed
debug
amkram
committed
rollinghash
AlanZhangUCSC
committed
up
AlanZhangUCSC
committed
refactor: Improve CMakeLists.txt for conciseness, clarity, and best practices
amkram
committed
debugging
amkram
committed
feat: add basic web server control panel for debugging panmap with genome, seeds, and mutations display
amkram
committed
feat: add web server integration to panmap in main.cpp
amkram
committed
feat: integrate web server and data export functionality into panmap
amkram
committed
fix: include header for blockStrand_t definition in pmi.cpp
amkram
committed
feat: add control panel debug page with new route and template
amkram
committed
feat: display node genome, aligned seeds, and mutations on control panel debug page
amkram
committed
feat: update data structure in data.json and remove placeholder logic in app.py for node genome display
amkram
committed
feat: send live data to web server during DFS in pmi.cpp and update Flask app to handle incoming data
amkram
committed
fix: move default argument for stop_coord to function declaration in header file
amkram
committed
feat: update exportDataToJson to include actual genome, seeds, and mutations in JSON output
amkram
committed
feat: implement debug web panel for panmap run with dynamic data updates
amkram
committed
feat: add interactive genome and seeds visualization using D3.js in web application
amkram
committed
feat: add nlohmann/json library and declare missing functions in main.cpp and app.py
amkram
committed
fix: link nlohmann/json library to panmap target in CMakeLists.txt
amkram
committed
fix: resolve compilation errors related to incorrect pointer usage and JSON push_back method in pmi.cpp
amkram
committed
feat: implement startWebServer function to launch Flask web server
amkram
committed
feat: implement exportDataToJson function in C++ and Python to export tree data to JSON format
amkram
committed
fix: include nlohmann/json library in main.cpp to resolve undeclared identifier errors
amkram
committed
fix: link cURL library to resolve undefined reference errors in panmap target
amkram
committed
fix: update path to web_server/app.py in main.cpp to resolve file not found error
amkram
committed
style: remove unnecessary blank line in main.cpp
amkram
committed
feat: enhance web server to render genome sequences and align seeds correctly
amkram
committed
fix: remove undefined references to T and filename in get_data function
amkram
committed
feat: keep panmap application running after execution completion
amkram
committed
fix: update path to web_server/app.py in startWebServer function in src/main.cpp
amkram
committed
fix: update web server path to correct location of app.py
amkram
committed
feat: copy web_server directory to build directory after panmap build
amkram
committed
fix: correct placement of app.run() to ensure Flask server starts when script is executed directly
amkram
committed
fix: allow Flask app to accept connections from any host to resolve HTTP 403 error
amkram
committed
build: expose port 5000 in Dockerfile for Flask web server access
amkram
committed
feat: add devcontainer configuration for CMake project in Docker
amkram
committed
feat: forward port 5000 for Flask web server accessibility in dev container
amkram
committed

Commits on Sep 3, 2024

fix
AlanZhangUCSC
committed
fix
AlanZhangUCSC
committed

Commits on Sep 4, 2024

Commits on Sep 9, 2024

Commits on Sep 10, 2024

Commits on Sep 11, 2024

Commits on Sep 12, 2024

Commits on Sep 17, 2024

adding mgsr
AlanZhangUCSC
committed

Commits on Sep 23, 2024

getting correct placement kminmers
AlanZhangUCSC
committed

Commits on Sep 24, 2024

kminmers from fastq
AlanZhangUCSC
committed

Commits on Sep 25, 2024

Commits on Sep 26, 2024

up
amkram
committed

Commits on Sep 27, 2024

Commits on Sep 30, 2024

oops
AlanZhangUCSC
committed

Commits on Oct 1, 2024

Commits on Oct 2, 2024

Commits on Oct 6, 2024

Commits on Oct 7, 2024

Commits on Oct 9, 2024

argfix
amkram
committed
merg
amkram
committed

Commits on Oct 11, 2024

partially multithreading
AlanZhangUCSC
committed

Commits on Oct 14, 2024

Commits on Oct 15, 2024

Commits on Oct 16, 2024

trying out multithreading EM
AlanZhangUCSC
committed

Commits on Oct 18, 2024

Commits on Oct 22, 2024

Commits on Oct 23, 2024

Commits on Oct 30, 2024

bwa to mpileup
AlanZhangUCSC
committed

Commits on Oct 31, 2024

random seed for simulater
AlanZhangUCSC
committed

Commits on Nov 1, 2024

haplotype-filtering
AlanZhangUCSC
committed

Commits on Nov 4, 2024

genotyping eval
AlanZhangUCSC
committed

Commits on Nov 6, 2024

Commits on Nov 7, 2024

fix read seedmers iorder
AlanZhangUCSC
committed

Commits on Nov 12, 2024

account for the edge case when a node has empty genome
AlanZhangUCSC
committed

Commits on Nov 13, 2024

fix ambiguous ref
AlanZhangUCSC
committed

Commits on Nov 14, 2024

fixed simulate seed type
genicos
committed

Commits on Nov 20, 2024

edit
AlanZhangUCSC
committed

Commits on Nov 22, 2024

up
AlanZhangUCSC
committed

Commits on Nov 25, 2024

fix
AlanZhangUCSC
committed
add more error messages
AlanAlohaUCSC
committed
merging
AlanAlohaUCSC
committed
unresolved merge
AlanAlohaUCSC
committed
fix again
AlanAlohaUCSC
committed

Commits on Nov 26, 2024

fix
AlanZhangUCSC
committed

Commits on Dec 13, 2024

Commits on Jan 13, 2025

Commits on Jan 15, 2025

Commits on Jan 16, 2025

Commits on Jan 18, 2025

Commits on Jan 21, 2025

Commits on Feb 3, 2025

try
amkram
committed
try
amkram
committed

Commits on Feb 13, 2025

Commits on Feb 27, 2025

Commits on Feb 28, 2025

Commits on Apr 10, 2025

Commits on May 26, 2025

interm
amkram
committed

Commits on Jun 12, 2025

fix endPos
amkram
committed

Commits on Jul 3, 2025

baba
amkram
committed

Commits on Jul 4, 2025

wrok
amkram
committed
prog
amkram
committed

Commits on Jul 5, 2025

to
amkram
committed
b
amkram
committed

Commits on Jul 8, 2025

index work?
amkram
committed

Commits on Jul 12, 2025

epicness
amkram
committed
helloAlan
amkram
committed

Commits on Jul 14, 2025

mutation matrix stuff
AlanZhangUCSC
committed

Commits on Jul 17, 2025

Commits on Jul 18, 2025