Misc improvements before index optimisation PR #339

leoisl · 2023-07-18T09:53:12Z

This PR contains several misc small fixes:

Fixes a segfault bug with getting the wrong pangraph node, introduced in the previous PR;
Fixes a minor bug that caused unmapped reads to be suppressed in the file SAM;
Removes the --clean command line option, redundant now that gene-DBGs code were removed;
Adds CLI option --rng-seed to make multimapping deterministic, if required;
A handful of clean ups of unused code;

include/utils.h

src/utils.cpp

leoisl · 2023-07-18T15:52:50Z

@mbhall88 feel free to comment on this, I can still incorporate changes

src/random_main.cpp

leoisl added 10 commits July 17, 2023 12:16

Fixing segfault bug with getting the wrong pangraph node

831f15a

Now outputting unmapped reads back in SAM

04b492e

Removing --clean command line option

9668275

Adding CLI option --rng-seed

db29469

Improving MinimizerHitClusters to accept RNG seeds

b7a4e97

Cleaning up unused code

4a8a20e

Improving position and section of --rng-seed parameter

0041e59

random_main now using std::mt19937 as random number generator

6d1e3be

Removing unused argument genome_size from get_minimizer_hit_clusters()

8bfbdb6

Fixing small issue in random_path()

e0881e8

leoisl requested review from mbhall88, iqbal-lab and Danderson123 July 18, 2023 09:53

iqbal-lab reviewed Jul 18, 2023

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iqbal-lab reviewed Jul 18, 2023

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iqbal-lab merged commit 57e3380 into iqbal-lab-org:dev Jul 18, 2023
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mbhall88 reviewed Jul 18, 2023

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leoisl deleted the misc branch November 2, 2023 10:02

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