Code

Update simulations for larger genomes#60

Code

Merged

andrewdavidsmith merged 14 commits intomastersmithlabcode/abismal:masterfrom update-for-large-simulationssmithlabcode/abismal:update-for-large-simulationsCopy head branch name to clipboardOct 27, 2024

+429-327

Commits

Commits on Oct 24, 2024

• src/simreads.cpp: refactoring loops so that the memory footprint does not grow with the size of the simulation

  andrewdavidsmith

  committed
  afe9f79

Commits on Oct 25, 2024

• src/simreads.cpp: adding option to output in FASTA format which helps for speed and disk footprint when running tests on massive simulated test data sets

  andrewdavidsmith

  committed
  2283443

• data/md5sum.txt: updating test output hashes for changes to order of operations within simreads, which causes the rng to be used in a different order and changes the random output

  andrewdavidsmith

  committed
  811806e

• Fixed differences in md5um.txt file from merge

  andrewdavidsmith

  committed
  24973f2

• src/abismal.cpp: adding version number in help output for abismal

  andrewdavidsmith

  committed
  d594e66

• src/abismalidx.cpp: reporting version with help message

  andrewdavidsmith

  committed
  d39e5a8

• src/simreads.cpp: setting default simulation behavior to allowing non-ACGT bases within fragments

  andrewdavidsmith

  committed
  ea2ec35

• src/abismalidx.cpp and src/abismal.cpp: cleaning up version and help printing stuff

  andrewdavidsmith

  committed
  fbdaced

• src/simreads.cpp: fixing major bug when trying to write locations for simulated reads

  andrewdavidsmith

  committed
  8921c59

Commits on Oct 26, 2024

• src/simreads.cpp: using uint64_t for the position of the simulated read in the genome because otherwise it was not enough for the human genome

  andrewdavidsmith

  committed
  45460a4

• src/simreads.cpp: code formatting

  andrewdavidsmith

  committed
  49a9719

• src/simreads.cpp: trying to debug an issue with integer values that seems to prevent simulating all the way through the human genome

  andrewdavidsmith

  committed
  1cbbac1

Commits on Oct 27, 2024

• src/simreads.cpp: apparently found the bug and it involved returning the int from the rng, despite the values generated by the rng being larger and the values it got assigned to being larger, they …

  Show description for 80a2d95
  andrewdavidsmith

  committed
  80a2d95

• data/md5sum.txt: updating test output file hashes for changes in rng from simulations

  andrewdavidsmith

  committed
  6c03831