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Update simulations for larger genomes #60

Merged
merged 14 commits into from
Oct 27, 2024
Merged

Update simulations for larger genomes #60

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afe9f79
src/simreads.cpp: refactoring loops so that the memory footprint does…
andrewdavidsmith Oct 24, 2024
2283443
src/simreads.cpp: adding option to output in FASTA format which helps…
andrewdavidsmith Oct 25, 2024
811806e
data/md5sum.txt: updating test output hashes for changes to order of …
andrewdavidsmith Oct 25, 2024
24973f2
Fixed differences in md5um.txt file from merge
andrewdavidsmith Oct 25, 2024
d594e66
src/abismal.cpp: adding version number in help output for abismal
andrewdavidsmith Oct 25, 2024
d39e5a8
src/abismalidx.cpp: reporting version with help message
andrewdavidsmith Oct 25, 2024
ea2ec35
src/simreads.cpp: setting default simulation behavior to allowing non…
andrewdavidsmith Oct 25, 2024
fbdaced
src/abismalidx.cpp and src/abismal.cpp: cleaning up version and help …
andrewdavidsmith Oct 25, 2024
8921c59
src/simreads.cpp: fixing major bug when trying to write locations for…
andrewdavidsmith Oct 25, 2024
45460a4
src/simreads.cpp: using uint64_t for the position of the simulated re…
andrewdavidsmith Oct 26, 2024
49a9719
src/simreads.cpp: code formatting
andrewdavidsmith Oct 26, 2024
1cbbac1
src/simreads.cpp: trying to debug an issue with integer values that s…
andrewdavidsmith Oct 26, 2024
80a2d95
src/simreads.cpp: apparently found the bug and it involved returning …
andrewdavidsmith Oct 27, 2024
6c03831
data/md5sum.txt: updating test output file hashes for changes in rng …
andrewdavidsmith Oct 27, 2024
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30 changes: 15 additions & 15 deletions data/md5sum.txt
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
ae8e662c3ab23ba742a45a9784390e63 tests/reads_1.fq
ddeea92ba05c5c6a909c136d5059140d tests/reads.mstats
7c43e9b1409c6725c70aeb18d8db3413 tests/reads_pbat_pe_1.fq
21c3b088e956de62e10a6d190ffb8744 tests/reads_pbat_pe_2.fq
8c170b022512012f078396cc19c41600 tests/reads_pbat_pe.mstats
ae8e662c3ab23ba742a45a9784390e63 tests/reads_pe_1.fq
d2723d2e99d2a3492af508633d61b30a tests/reads_pe_2.fq
6e2ba01e98f0effc005641ba6a7eb8b6 tests/reads_pe.mstats
2e033e6c0f2e93000877d6f8f40bcc99 tests/reads_rpbat_pe_1.fq
a28bc47b567130bbcdc45b1daa54ae32 tests/reads_rpbat_pe_2.fq
ecf7559bdeecb3f5d23e2c85e1eb22ff tests/reads_rpbat_pe.mstats
8dc13cfc9c7af9c5ed368d5e2462275e tests/reads_1.fq
04f73fa36d90fbe9e157e5c3214e585a tests/reads.mstats
da3003dc18e6ecfcf0586705444ca6f8 tests/reads_pbat_pe_1.fq
bbfd18b0cc7cf93ad4ed317ef996f3ee tests/reads_pbat_pe_2.fq
7d2e72d75fe2e55f978dffa76a492c61 tests/reads_pbat_pe.mstats
2415d44925cc23fa60a0d78c9af04509 tests/reads_pbat_pe.sam
d49efb9f420b4edeb4647217fa247e6d tests/reads_pe_1.fq
3627c807f259109ea0c4c2b7bcd12320 tests/reads_pe_2.fq
0efe8fb80106f2edb370e8f7e7c1bbb6 tests/reads_pe.mstats
3c10bd0ce3f7d458a05a334a351d96ff tests/reads_pe.sam
3dd98274d8b707878aaad8246c6df9f6 tests/reads_rpbat_pe_1.fq
fcf5e4d93ac62dafcfb279e95103ad0e tests/reads_rpbat_pe_2.fq
19329a8ec659a82dc82e56a0ca6999b0 tests/reads_rpbat_pe.mstats
c6980b863b86d7e491e3f9358943bcd3 tests/reads_rpbat_pe.sam
0f2ad3720fd50961494222a3cf1dbef1 tests/reads.sam
bcbf01be810cbf4051292813eb6b9225 tests/tRex1.idx
411a91bbd43a429ca665e350ddb96c4b tests/reads_pbat_pe.sam
28312ec7f684e8552be4a842e451e9be tests/reads_rpbat_pe.sam
7a1dd56c17759819bdc6cca3cf39ef1d tests/reads.sam
a067f22b83e6a7cd1246cdc0353b7ce9 tests/reads_pe.sam
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