Fix: improve region query logic in RAMNTupleView by AdityaPandeyCN · Pull Request #15 · compiler-research/ramtools

AdityaPandeyCN · 2026-02-01T19:11:45Z

Add CIGAR span calculation for accurate read overlap detection
Filter secondary/supplementary/unmapped reads (flag 0x904)
Support reference name aliasing (chr1 <-> 1, chrM <-> MT)
Handle flexible query formats (rname, rname:pos, rname:start-end, *)
Use individual field views for better performance
Add early termination when past query region

codecov-commenter · 2026-02-01T19:15:23Z

Codecov Report

❌ Patch coverage is 80.76923% with 35 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (develop@83334a1). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
test/ramcoretests.cxx	71.91%	0 Missing and 25 partials ⚠️
src/ramcore/RAMNTupleView.cxx	87.01%	2 Missing and 8 partials ⚠️

❌ Your patch status has failed because the patch coverage (80.76%) is below the target coverage (85.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@            Coverage Diff             @@
##             develop      #15   +/-   ##
==========================================
  Coverage           ?   55.78%           
==========================================
  Files              ?       16           
  Lines              ?     1425           
  Branches           ?      752           
==========================================
  Hits               ?      795           
  Misses             ?      521           
  Partials           ?      109

Flag	Coverage Δ
unittests	`55.78% <80.76%> (?)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
benchmark/generate_sam.cxx	`92.72% <100.00%> (ø)`
src/ramcore/RAMNTupleView.cxx	`88.63% <87.01%> (ø)`
test/ramcoretests.cxx	`73.95% <71.91%> (ø)`

Files with missing lines	Coverage Δ
benchmark/generate_sam.cxx	`92.72% <100.00%> (ø)`
src/ramcore/RAMNTupleView.cxx	`88.63% <87.01%> (ø)`
test/ramcoretests.cxx	`73.95% <71.91%> (ø)`

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github-actions

clang-tidy made some suggestions

github-actions

clang-tidy made some suggestions

github-actions · 2026-02-02T08:08:46Z

+
+} // namespace
+
+Long64_t ramntupleview(const char *file, const char *query, bool /*cache*/, bool /*perfstats*/,


warning: function 'ramntupleview' can be made static or moved into an anonymous namespace to enforce internal linkage [misc-use-internal-linkage]

Suggested change

Long64_t ramntupleview(const char *file, const char *query, bool /*cache*/, bool /*perfstats*/,

Long64_t ramntupleviewstatic (const char *file, const char *query, bool /*cache*/, bool /*perfstats*/,

vgvassilev · 2026-02-02T11:36:18Z

Codecov Report

❌ Patch coverage is 46.57534% with 39 lines in your changes missing coverage. Please review. ⚠️ Please upload report for BASE (develop@ef5b3ae). Learn more about missing BASE report.
Files with missing lines Patch % Lines
src/ramcore/RAMNTupleView.cxx 46.57% 27 Missing and 12 partials ⚠️

❌ Your patch status has failed because the patch coverage (46.57%) is below the target coverage (85.00%). You can increase the patch coverage or adjust the target coverage.
Additional details and impacted files

🚀 New features to boost your workflow:

In a separate PR, we should make codecov block PRs if the testing coverage degrades.

github-actions

clang-tidy made some suggestions

github-actions

clang-tidy made some suggestions

AdityaPandeyCN · 2026-02-11T08:16:26Z

Can you have a look @vgvassilev ?

vgvassilev · 2026-02-11T09:33:40Z

Can you address the clang-tidy and missing coverage first?

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 10 out of 13. Check the log or trigger a new build to see more.

github-actions

clang-tidy made some suggestions

github-actions · 2026-02-13T14:25:59Z

+
+      if (i < 10) {
+         chrom = "chr1";
+         chrom_length = 249250621;


warning: Value stored to 'chrom_length' is never read [clang-analyzer-deadcode.DeadStores]

chrom_length = 249250621; ^

Additional context

benchmark/generate_sam.cxx:52: Value stored to 'chrom_length' is never read

chrom_length = 249250621; ^

github-actions

clang-tidy made some suggestions

github-actions · 2026-02-13T15:08:10Z

@@ -1,3 +1,4 @@
+#include <cstdint>
 #include <gtest/gtest.h>


warning: 'gtest/gtest.h' file not found [clang-diagnostic-error]

#include <gtest/gtest.h> ^

That's an issue which needs to be fixed in clang-tidy as we discussed.

github-actions

clang-tidy made some suggestions

AdityaPandeyCN · 2026-02-16T12:27:35Z

Hi @vgvassilev , Can you have a look? Code cov of the test file should not be a issue and the ntupleview file is now above the required no.

vgvassilev

There is still some relevant clang-tidy issues. Also this looks broken: https://app.codecov.io/gh/compiler-research/ramtools/pull/15?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compiler-research

vgvassilev · 2026-02-18T11:00:02Z

+   std::string rest = region.substr(colonPos + 1);
+
+   size_t dashPos = rest.find('-');
+   try {


Is it a good idea to rely on exceptions for this code?

Removed try-catch exceptions

vgvassilev · 2026-02-18T11:01:12Z

@@ -1,3 +1,4 @@
+#include <cstdint>
 #include <gtest/gtest.h>


That's an issue which needs to be fixed in clang-tidy as we discussed.

github-actions

clang-tidy made some suggestions

AdityaPandeyCN · 2026-02-18T13:27:44Z

I guess codecov problem is it doesn't has a successful base commit to compare against, this PR would solve it(https://docs.codecov.com/docs/error-reference#section-missing-head-commit)

AdityaPandeyCN · 2026-03-02T10:20:13Z

@vgvassilev Can we get this in?

vgvassilev

LGTM! Please squash everything into a single commit with the appropriate commit message.

- Add CIGAR span calculation for accurate read overlap detection - Filter secondary/supplementary/unmapped reads (flag 0x904) - Support reference name aliasing (chr1 <-> 1, chrM <-> MT) - Handle flexible query formats (rname, rname:pos, rname:start-end, *) - Use individual field views for better performance - Add early termination when past query region Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

AdityaPandeyCN · 2026-03-04T11:07:29Z

@vgvassilev Squashed the commits!

AdityaPandeyCN · 2026-03-06T03:58:37Z

@vgvassilev Gentle reminder for this

- Add CIGAR span calculation for accurate read overlap detection - Filter secondary/supplementary/unmapped reads (flag 0x904) - Support reference name aliasing (chr1 <-> 1, chrM <-> MT) - Handle flexible query formats (rname, rname:pos, rname:start-end, *) - Use individual field views for better performance - Add early termination when past query region Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> use enums and add tests Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> clang formatting Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> add comments Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> clang formatting Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com> clang formatting Signed-off-by: AdityaPandeyCN <adityapand3y666@gmail.com>

github-actions Bot reviewed Feb 1, 2026

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Comment thread src/ramcore/RAMNTupleView.cxx

Comment thread src/ramcore/RAMNTupleView.cxx

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AdityaPandeyCN marked this pull request as draft February 2, 2026 11:57

github-actions Bot reviewed Feb 4, 2026

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Comment thread src/ramcore/RAMNTupleView.cxx

Comment thread test/ramcoretests.cxx

Comment thread test/ramcoretests.cxx

Comment thread test/ramcoretests.cxx Outdated

AdityaPandeyCN marked this pull request as ready for review February 4, 2026 08:24

github-actions Bot reviewed Feb 4, 2026

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Comment thread src/ramcore/RAMNTupleView.cxx

AdityaPandeyCN marked this pull request as draft February 13, 2026 13:15

github-actions Bot reviewed Feb 13, 2026

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github-actions Bot reviewed Feb 16, 2026

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Comment thread test/ramcoretests.cxx

Comment thread test/ramcoretests.cxx

AdityaPandeyCN marked this pull request as ready for review February 16, 2026 11:41

vgvassilev reviewed Feb 18, 2026

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github-actions Bot reviewed Feb 18, 2026

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Comment thread src/ramcore/RAMNTupleView.cxx

AdityaPandeyCN mentioned this pull request Mar 4, 2026

Tracking Bug fixes and Feature addition in ramtools project #24

Open

5 tasks

vgvassilev approved these changes Mar 4, 2026

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AdityaPandeyCN force-pushed the ramcore_fix branch from 7a8c111 to d77d340 Compare March 4, 2026 10:29

Merge upstream/develop

cef6ab1

AdityaPandeyCN force-pushed the ramcore_fix branch 2 times, most recently from 90f9f2c to cef6ab1 Compare March 4, 2026 11:01

vgvassilev merged commit 4504216 into compiler-research:develop Mar 6, 2026
8 checks passed


		} // namespace

		Long64_t ramntupleview(const char file, const char query, bool /cache/, bool /perfstats/,

	Long64_t ramntupleview(const char file, const char query, bool /cache/, bool /perfstats/,
	Long64_t ramntupleviewstatic (const char file, const char query, bool /cache/, bool /perfstats/,

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