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Updates including fix for roi on counts-nano output and move to strict SAM as assumed in format command #299

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Merged
andrewdavidsmith merged 11 commits into from
Oct 7, 2025
Merged

Updates including fix for roi on counts-nano output and move to strict SAM as assumed in format command #299

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2708965
src/utils/uniq.cpp: computing the derived values when they are printe…
andrewdavidsmith Sep 27, 2025
7f30aad
src/analysis/bsrate.cpp: computing the derived values when they are p…
andrewdavidsmith Sep 27, 2025
90d19ce
src/common/LevelsCounter.hcpp: made functions for mean_depth, mean_de…
andrewdavidsmith Oct 7, 2025
cfddf69
src/abismal: updating submodule
andrewdavidsmith Oct 7, 2025
bf18742
src/common/LevelsCounter.hcpp: renamed sites_covered_fraction to site…
andrewdavidsmith Oct 7, 2025
c0f3728
src/analysis/hmr.cpp: cleanup
andrewdavidsmith Oct 7, 2025
b9e6262
src/utils/format-reads.cpp: now requiring that the input be given as …
andrewdavidsmith Oct 7, 2025
5fba078
src/utils/format-reads.cpp: fixing a bug of negative of negative
andrewdavidsmith Oct 7, 2025
c2ae487
src/common/LevelsCounter.cpp: cleanup
andrewdavidsmith Oct 7, 2025
028716d
src/analysis/roimethstat.cpp: allowing an option for extra cols in ou…
andrewdavidsmith Oct 7, 2025
8dff276
data/md5sum.txt: updates for changes to abismal submodule and very mi…
andrewdavidsmith Oct 7, 2025
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6 changes: 3 additions & 3 deletions data/md5sum.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,6 @@ e73facd597c3b903cbfe29afa9f58371 tests/reads.counts
0f72560aa101e85679783a1ecaf80615 tests/reads.epiread
9dbd476424d48a8d0f043dfc00af0d23 tests/reads.fmt.srt.sam
4085cc74b003a918b4a4743fca7922a4 tests/reads.hmr
5c6fbbc6e565f23afa4f597f2483acb0 tests/reads.levels
a389e4ee1687895517b0b0d26e9338ee tests/reads.mstats
d8856f9731af76b8a4ab3cc7d667cdb2 tests/reads.ustats
bcbf01be810cbf4051292813eb6b9225 tests/tRex1.idx
ec6a686617cad31e9f7a37a3d378e6ed tests/two_epialleles.states
Expand All @@ -17,8 +15,10 @@ d947fe3d61ef7b1564558a69608f0e64 tests/methylome.pmd
d41d8cd98f00b204e9800998ecf8427e tests/two_epialleles.amr
001b9d966f62fa439b24cf2198cc3de5 tests/reads.counts.sym
2b8a0406015458be51b8b1c9e58b3602 tests/tRex1_promoters.roi.bed
9bdb361091d1c0626df30be8ba2c408c tests/reads.sam
33640b24cb64ad3179f364af5a887f95 tests/reads.fmt.sam
b5a63997c57dcde5c3a6635f7beb2cce tests/reads.fmt.srt.uniq.sam
3ac2b51545740bafd1a548ba7f73e739 tests/reads.xcounts
054fe804a32063c80862fbee30f74579 tests/reads.unxcounts
830157684f1ddbf1f1c37d354188dc2b tests/reads.sam
8dbcdabecb6cfe6aebb73c94c605f696 tests/reads.mstats
490723e9af084c8f957f5a265cf02994 tests/reads.levels
2 changes: 1 addition & 1 deletion src/abismal
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Submodule abismal updated 2 files
+8 −8 data/md5sum.txt
+276 −383 src/abismal.cpp
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