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samtools/samtools
2235
samtools__samtools-2235
[ "1563" ]
abaa1583614a12cb446e8927b92723fdfde2025c
diff --git a/coverage.c b/coverage.c index 92f497dc8..7fcb34f7e 100644 --- a/coverage.c +++ b/coverage.c @@ -1,7 +1,7 @@ /* coverage.c -- samtools coverage subcommand Copyright (C) 2018,2019 Florian Breitwieser - Portions copyright (C) 2019-2021, 2023-2024 Genome Research Ltd. + Portions copyright (C) 201...
diff --git a/test/coverage/1.expected b/test/coverage/1.expected new file mode 100644 index 000000000..35cd07c2a --- /dev/null +++ b/test/coverage/1.expected @@ -0,0 +1,3 @@ +#rname startpos endpos numreads covbases coverage meandepth meanbaseq meanmapq +T1 1 40 6 19 47.5 0.725 7.62 36.7 +T2 1 40 6 8 20 0.4 7.12 49 dif...
Minimum depth threshold for "samtools coverage"? #### Is your feature request related to a problem? Please specify. I'd like a simple way to calculate the coverage stats for a bam file. The closest out-of-the-box thing I can find is `samtools coverage`. I run the command like so: ``` samtools coverage input.bam ...
Looks like a good idea, we'll consider it. Hi Did you implement it in Samtools? It doesn't look it, but this line is the thing you could manually tweak in a local copy: https://github.com/samtools/samtools/blob/develop/coverage.c#L603 If changed to `>=10` for example it'd need a minimum of 10 deep. However loo...
Looks like a good idea, we'll consider it. Hi Did you implement it in Samtools? It doesn't look it, but this line is the thing you could manually tweak in a local copy: https://github.com/samtools/samtools/blob/develop/coverage.c#L603 If changed to `>=10` for example it'd need a minimum of 10 deep. However loo...
[ "https://github.com/samtools/samtools/commit/3a769cfa9a71df943b00068566a171269e2789d3", "https://github.com/samtools/samtools/commit/6a807af098c28ef534b684aaa2b305e5776145d2" ]
2025-07-10T19:03:03Z
https://github.com/samtools/samtools/tree/abaa1583614a12cb446e8927b92723fdfde2025c
[ "autoheader && autoconf -Wno-syntax ; ./configure --with-htslib=htslib ; make" ]
[ "make test V=1 2>&1 | tee test-output.log" ]
[ "cat test-output.log" ]
def parser(log: str) -> dict[str, str]: import re results = {} # Match lines like: test_name: <command> .. ok / .. failed test_re = re.compile(r'^(?P<name>[^\s].*?):\s*$') status_re = re.compile(r'^\.\. (ok|failed)', re.IGNORECASE) current_test = None for line in log.splitlines(): m...
[ "test_coverage" ]
[ "test_large_positions", "test_merge", "test_collate", "test_reference", "test_split", "test_quickcheck", "test_markdup", "test_bedcov", "test_reheader", "test_addrprg", "test_sort", "test_dict", "test_head", "test_fixmate", "test_stats", "test_idxstat", "test_ampliconclip", "test_i...
starryzhang/sweb.eval.x86_64.samtools_1776_samtools-2235
micropython/micropython
17683
micropython__micropython-17683
[ "17657" ]
554f114f181ee942ee3c74e44cef653604abbaef
diff --git a/ports/webassembly/objpyproxy.js b/ports/webassembly/objpyproxy.js index 0eafd0dec53de..64703d78a5589 100644 --- a/ports/webassembly/objpyproxy.js +++ b/ports/webassembly/objpyproxy.js @@ -165,34 +165,35 @@ const py_proxy_handler = { if (prop === "_ref") { return target._ref; ...
diff --git a/tests/ports/webassembly/py_proxy_get.mjs b/tests/ports/webassembly/py_proxy_get.mjs new file mode 100644 index 0000000000000..825de7cabeb78 --- /dev/null +++ b/tests/ports/webassembly/py_proxy_get.mjs @@ -0,0 +1,14 @@ +// Test `<py-obj> get <attr>` on the JavaScript side, which tests PyProxy.get. + +const ...
webassembly: getting JS symbols implicitly also throws errors ### Port, board and/or hardware webassembly ### MicroPython version MicroPython webassembly latest from *npm* ### Reproduction In here we solved the `in` operation check https://github.com/micropython/micropython/pull/17604 but if any libraries tries to...
thanks @dpgeorge , any chance this can make it to npm too?
[ "https://github.com/micropython/micropython/commit/c72a3e528d7909c212596b52de5f9a5fe0161f17" ]
2025-07-15T08:45:08Z
https://github.com/micropython/micropython/tree/554f114f181ee942ee3c74e44cef653604abbaef
[ "make -C mpy-cross ; make -C ports/unix" ]
[ "make -C ports/unix test 2>&1 | tee test-output.log" ]
[ "cat test-output.log" ]
def parser(log: str) -> dict[str, str]: import re results: dict[str, str] = {} for line in log.splitlines(): m = re.match(r'(pass|FAIL|skip)\s+(\S+)', line) if m: status_word, test_name = m.groups() status_word = status_word.lower() if status_word == "pass...
[ "micropython/heapalloc_fail_dict.py", "micropython/heapalloc_int_from_bytes.py", "float/float_divmod.py", "extmod/json_load.py", "extmod/re1.py", "float/cmath_dunder.py", "extmod/vfs_userfs.py", "float/builtin_float_minmax.py", "float/lexer.py", "basics/struct1.py", "basics/try_else.py", "micr...
[ "basics/memoryview1.py", "basics/int_big_rshift.py", "io/file_stdio.py", "extmod/re_sub.py", "basics/bytearray_construct_endian.py", "basics/dict_fromkeys.py", "micropython/viper_binop_arith_uint.py", "misc/non_compliant_lexer.py", "basics/int_big_add.py", "io/file_stdio2.py", "basics/class_dict...
starryzhang/sweb.eval.x86_64.micropython_1776_micropython-17683
timescale/timescaledb
8559
timescale__timescaledb-8559
[ "6902" ]
bbbebbfa978465bfdf6d0bac418ee4d269ad4da8
diff --git a/.unreleased/pr_8559 b/.unreleased/pr_8559 new file mode 100644 index 00000000000..79123483309 --- /dev/null +++ b/.unreleased/pr_8559 @@ -0,0 +1,2 @@ +Fixes: #8559 Fix `timestamp out of range` using `end_offset=NULL` on CAgg refresh policy +Thanks: @nofalx for reporting the error when using `end_offset=NUL...
diff --git a/tsl/test/expected/cagg_policy.out b/tsl/test/expected/cagg_policy.out index aaa6d5b8621..d85f7f4a24c 100644 --- a/tsl/test/expected/cagg_policy.out +++ b/tsl/test/expected/cagg_policy.out @@ -1400,3 +1400,72 @@ SELECT timescaledb_experimental.add_policies('cagg'); f (1 row) +-- Issue #6902 +-- Fix tim...
[Bug]: Continuous aggregates with time_bucket hourly and timezone fail to update ### What type of bug is this? Incorrect result, Unexpected error ### What subsystems and features are affected? Continuous aggregate ### What happened? I have a number of Continuous aggregates that uses hourly buckets ``` time_buck...
Thanks for the script, it reproduces for me. The error is related to the NULL value of the `end_offset`, so probably as a workaround you can set it to something far in the future but not null. @fabriziomello should the end point calculation follow the same logic as `cagg_get_time_min`? Currently the null end point...
Thanks for the script, it reproduces for me. The error is related to the NULL value of the `end_offset`, so probably as a workaround you can set it to something far in the future but not null. @fabriziomello should the end point calculation follow the same logic as `cagg_get_time_min`? Currently the null end point...
[ "https://github.com/timescale/timescaledb/commit/e39f398c62e9d3271ad15179f46aa4985ea54f4a" ]
2025-08-28T23:08:57Z
https://github.com/timescale/timescaledb/tree/bbbebbfa978465bfdf6d0bac418ee4d269ad4da8
[ "cmake --build build --parallel ; make -C build install" ]
[ "PATH=$PATH:/usr/lib/postgresql/17/bin pkill -u postgres postgres || true && rm -rf /tmp/pgdata && chown -R postgres:postgres /testbed/build && su - postgres -c \"PATH=$PATH:/usr/lib/postgresql/17/bin make -C /testbed/build installcheck\" 2>&1 | tee test-output.log" ]
[ "cat test-output.log" ]
def parser(log: str) -> dict[str, str]: import re results = {} for line in log.splitlines(): m = re.match(r'(ok|not ok)\s+\d+\s+\+?\s*([^\s]+)', line) if m: status_word, test_name = m.groups() status = "pass" if status_word == "ok" else "fail" results[test...
[ "cagg_policy" ]
[ "compression_qualpushdown", "chunk_column_stats", "cagg_deprecated_bucket_ng", "compress_default", "cagg_refresh_using_trigger", "cagg_policy_concurrent", "compression_sorted_merge", "modify_exclusion", "ordered_append-17", "compress_auto_sparse_index", "vector_agg_groupagg", "merge_append_par...
starryzhang/sweb.eval.x86_64.timescale_1776_timescaledb-8559
cilium/tetragon
4069
cilium__tetragon-4069
[ "4056" ]
67530967429bb42b665a7c7e69cdbc200247ccb4
"diff --git a/api/v1/README.md b/api/v1/README.md\nindex 6bf750caea6..85596fcf70f 100644\n--- a/api/(...TRUNCATED)
"diff --git a/pkg/process/podinfo_test.go b/pkg/process/podinfo_test.go\nindex 46dba2c18b0..b06ec51f(...TRUNCATED)
"Include pod UID in the log\n### Is there an existing issue for this?\n\n- [x] I have searched the e(...TRUNCATED)
"As discussed in Slack, to implement this you can get inspiration from this https://github.com/ciliu(...TRUNCATED)
"As discussed in Slack, to implement this you can get inspiration from this https://github.com/ciliu(...TRUNCATED)
[ "https://github.com/cilium/tetragon/commit/3d566e06298cffff24f369932ac92e59f3049878" ]
2025-08-29T05:43:42Z
https://github.com/cilium/tetragon/tree/67530967429bb42b665a7c7e69cdbc200247ccb4
[ "export PATH=/usr/local/go/bin:$PATH ; make vendor ; make tetragon" ]
[ "go test ./... -v 2>&1 | tee test-output.log" ]
[ "cat test-output.log" ]
"def parser(log: str) -> dict[str, str]:\n import re\n results = {}\n pattern = re.compile((...TRUNCATED)
[ "TestK8sWatcher_GetPodInfo", "TestProcessCache" ]
["TestTracepointFieldParsing","FuzzProtojsonCompatibility/636add9a0930f826","FuzzProtojsonCompatibil(...TRUNCATED)
starryzhang/sweb.eval.x86_64.cilium_1776_tetragon-4069
quickjs-ng/quickjs
1113
quickjs-ng__quickjs-1113
[ "1112" ]
3d3b58d8815f0eef8122fad142a65f3bd21d273b
"diff --git a/quickjs.c b/quickjs.c\nindex 8b9a3b573..01eb10123 100644\n--- a/quickjs.c\n+++ b/quick(...TRUNCATED)
"diff --git a/tests/test_builtin.js b/tests/test_builtin.js\nindex 3c37f5930..2e86cb4a2 100644\n--- (...TRUNCATED)
"Cannot extend TypedArray\nThis should work:\n```js\nvar TypedArray = Object.getPrototypeOf(Uint8Arr(...TRUNCATED)
[ "https://github.com/quickjs-ng/quickjs/commit/c5e673abf837fced6d324174d653dae7a8584814" ]
2025-06-24T20:23:51Z
https://github.com/quickjs-ng/quickjs/tree/3d3b58d8815f0eef8122fad142a65f3bd21d273b
[ "git submodule update --init --checkout --depth 1 ; make" ]
["./build/run-test262 -vv -m -a -c test262.conf -c test262-fast.conf test262 2>&1 | tee test-output.(...TRUNCATED)
[ "cat test-output.log" ]
"def parser(log: str) -> dict[str, str]:\n import re\n results: dict[str, str] = {}\n # Mat(...TRUNCATED)
["test262/test/language/expressions/class/dstr/async-gen-meth-dflt-ary-init-iter-get-err.js","test26(...TRUNCATED)
["test262/test/built-ins/Array/fromAsync/this-constructor-with-unsettable-element-closes-sync-iterat(...TRUNCATED)
starryzhang/sweb.eval.x86_64.quickjs-ng_1776_quickjs-1113
fluent/fluent-bit
10563
fluent__fluent-bit-10563
[ "10560" ]
c872957b57b2a8704e3b8cbc7f3994b430f96140
"diff --git a/plugins/out_loki/loki.c b/plugins/out_loki/loki.c\nindex 2bdcaba3539..ee7a4313a89 1006(...TRUNCATED)
"diff --git a/tests/runtime/out_loki.c b/tests/runtime/out_loki.c\nindex a440fc0b692..e177b01e675 10(...TRUNCATED)
"Inconsistent `Remove_Keys` behavior when running Loki output with multiple workers / threads\n## Bu(...TRUNCATED)
Wow, that was fast! Thanks!
["https://github.com/fluent/fluent-bit/commit/f54cd8193712aed8eb64af38928ed76ef76e619f","https://git(...TRUNCATED)
2025-07-09T04:16:04Z
https://github.com/fluent/fluent-bit/tree/c872957b57b2a8704e3b8cbc7f3994b430f96140
["cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release -DFLB_DEV=On -DFLB_TESTS_RUNTIME=On -DFLB_(...TRUNCATED)
[ "ctest --test-dir build --output-on-failure | tee test-output.log" ]
[ "cat test-output.log" ]
"def parser(log: str) -> dict[str, str]:\n import re\n results: dict[str, str] = {}\n # Mat(...TRUNCATED)
[ "flb-rt-out_stackdriver" ]
["flb-rt-out_null","flb-rt-out_stdout","flb-rt-core_accept_timeout","flb-rt-custom_calyptia_input_te(...TRUNCATED)
starryzhang/sweb.eval.x86_64.fluent_1776_fluent-bit-10563
php/php-src
19478
php__php-src-19478
[ "19476" ]
9c754baa99c795a65f40b94e4183150889895218
"diff --git a/NEWS b/NEWS\nindex 77c1e32ff3a82..0180f5b3478a6 100644\n--- a/NEWS\n+++ b/NEWS\n@@ -5,(...TRUNCATED)
"diff --git a/Zend/tests/pipe_operator_reference_context.phpt b/Zend/tests/pipe_operator_reference_c(...TRUNCATED)
"pipe operator (`|>`) fails to correctly handle returning by reference\n### Description\n\nThere app(...TRUNCATED)
[ "https://github.com/php/php-src/commit/784755f5defdcaee7b7265bbf5c2d2c1ec3d2e42" ]
2025-08-14T11:24:49Z
https://github.com/php/php-src/tree/9c754baa99c795a65f40b94e4183150889895218
["apt-get install -y pkg-config build-essential autoconf bison re2c libxml2-dev libsqlite3-dev ; ./c(...TRUNCATED)
[ "make test 2>&1 | tee test-output.log" ]
[ "cat test-output.log" ]
"def parser(log: str) -> dict[str, str]:\n import re\n results = {}\n # Match lines like: T(...TRUNCATED)
[ "Zend/tests/pipe_operator_reference_context.phpt" ]
["Zend/tests/dynamic_prop_deprecation_002.phpt","ext/standard/tests/strings/utf8.phpt","tests/lang/b(...TRUNCATED)
starryzhang/sweb.eval.x86_64.php_1776_php-src-19478
varnishcache/varnish-cache
4370
varnishcache__varnish-cache-4370
[ "4329" ]
c3b45a3140d340b2ed1a529b41253c2eb4ba70ae
"diff --git a/bin/varnishd/cache/cache_req_fsm.c b/bin/varnishd/cache/cache_req_fsm.c\nindex 8038102(...TRUNCATED)
"diff --git a/bin/varnishtest/tests/c00055.vtc b/bin/varnishtest/tests/c00055.vtc\nindex 0484219671.(...TRUNCATED)
"Bad chunked encoding should cause 400 error, not 503\n### Expected Behavior\n\nBad chunked encoding(...TRUNCATED)
bugwash agrees.
bugwash agrees.
["https://github.com/varnishcache/varnish-cache/commit/dbdf05e0b7ec5cb7d4f7f8e991ebc670e011c257","ht(...TRUNCATED)
2025-07-21T12:26:30Z
https://github.com/varnishcache/varnish-cache/tree/c3b45a3140d340b2ed1a529b41253c2eb4ba70ae
[ "./configure ; make -j$(nproc)" ]
[ "make check VERBOSE=1 2>&1 | tee test-output.log" ]
[ "cat test-output.log" ]
"def parser(log: str) -> dict[str, str]:\n import re\n results = {}\n for line in log.split(...TRUNCATED)
[ "tests/r02722.vtc", "tests/f00001.vtc", "tests/c00067.vtc", "tests/f00016.vtc", "tests/c00055.vtc" ]
["vtest2/tests/a00002.vtc","vtest2/tests/a02016.vtc","tests/b00073.vtc","tests/r00502.vtc","tests/r0(...TRUNCATED)
starryzhang/sweb.eval.x86_64.varnishcache_1776_varnish-cache-4370
rsyslog/rsyslog
6047
rsyslog__rsyslog-6047
[ "2424" ]
4b3ce60b76362c16f0bece97bafc57fe4aaa3922
"diff --git a/grammar/rainerscript.c b/grammar/rainerscript.c\nindex 82638305f4..b435b393f3 100644\n(...TRUNCATED)
"diff --git a/tests/rscript_random_warning.sh b/tests/rscript_random_warning.sh\nnew file mode 10075(...TRUNCATED)
"rainerscript: random() function does not provide user-visible warning when passed an unsupported va(...TRUNCATED)
[ "https://github.com/rsyslog/rsyslog/commit/2f62e6e76b961ae755d4103d60c010af42eedd7b" ]
2025-08-28T10:26:55Z
https://github.com/rsyslog/rsyslog/tree/4b3ce60b76362c16f0bece97bafc57fe4aaa3922
["autoreconf -fvi ; ./configure --enable-imfile --enable-mysql --enable-usertools --enable-pgsql --e(...TRUNCATED)
["./configure --enable-testbench --enable-imdiag --enable-omstdout && make -j$(nproc) && make check (...TRUNCATED)
[ "cat test-output.log" ]
"def parser(log: str) -> dict[str, str]:\n import re\n results = {}\n for line in log.split(...TRUNCATED)
[ "omfwd-lb-1target-retry-full_buf.sh" ]
["rscript_substring.sh","rscript_set_modify.sh","imuxsock_logger_err.sh","func-substring-invld-start(...TRUNCATED)
starryzhang/sweb.eval.x86_64.rsyslog_1776_rsyslog-6047
aws/s2n-tls
5481
aws__s2n-tls-5481
[ "5477" ]
795f4dc65335b56dfb356d6eaac9429fbae5b75b
"diff --git a/tls/s2n_auth_selection.c b/tls/s2n_auth_selection.c\nindex 5678f4ae82a..6971f9495e3 10(...TRUNCATED)
"diff --git a/tests/integrationv2/common.py b/tests/integrationv2/common.py\nindex 5b526a27fbd..2667(...TRUNCATED)
"s2n-tls server reports signature scheme with RSA kex\n### Security issue notifications\n\nIf you di(...TRUNCATED)
["https://github.com/aws/s2n-tls/commit/4f5133dc6c56030fd2b9691f75fd5e7f6259df09","https://github.co(...TRUNCATED)
2025-08-25T16:58:39Z
https://github.com/aws/s2n-tls/tree/795f4dc65335b56dfb356d6eaac9429fbae5b75b
["apt-get install -y libssl-dev ; cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release ; cmake --(...TRUNCATED)
[ "ctest --test-dir build --verbose 2>&1 | tee test-output.log" ]
[ "cat test-output.log" ]
"def parser(log: str) -> dict[str, str]:\n import re\n results: dict[str, str] = {}\n # Mat(...TRUNCATED)
[ "s2n_signature_algorithms_test", "s2n_handshake_test" ]
["s2n_client_signature_algorithms_extension_test","s2n_tls13_server_cert_test","s2n_client_session_t(...TRUNCATED)
starryzhang/sweb.eval.x86_64.aws_1776_s2n-tls-5481
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This is the multi - language version of swebench-Live.

We crawled GitHub issues as SWE tasks for coding agents to solve.

We used RepoLaunch to setup docker images as the problem-solving sandboxes for each instance.

Each split is task set of one language.

Each split is filtered by prompting LLM -- discarded if LLM cannot infer test patch from problem statement or problem statement contains solution (in NL or code).

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