fix: generalize sorting for pangenome mapped reads (#353) #1994
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10 warnings
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run workflow
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
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The 'defaults' channel might have been added implicitly. If this is intentional, add 'defaults' to the 'channels' list. Otherwise, consider setting 'conda-remove-defaults' to 'true'.
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warning libmamba [ca-certificates-2024.12.14-hbcca054_0] The following files were already present in the environment:
- ssl/cacert.pem
- ssl/cert.pem
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warning libmamba [ld_impl_linux-64-2.43-h712a8e2_2] The following files were already present in the environment:
- bin/x86_64-conda-linux-gnu-ld
- bin/x86_64-conda_cos6-linux-gnu-ld
- x86_64-conda-linux-gnu/bin/ld
- x86_64-conda_cos6-linux-gnu/bin/ld
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warning libmamba [tzdata-2025a-h78e105d_0] The following files were already present in the environment:
- share/zoneinfo/Africa/Abidjan
- share/zoneinfo/Africa/Accra
- share/zoneinfo/Africa/Addis_Ababa
- share/zoneinfo/Africa/Algiers
- share/zoneinfo/Africa/Asmara
- share/zoneinfo/Africa/Asmera
- share/zoneinfo/Africa/Bamako
- share/zoneinfo/Africa/Bangui
- share/zoneinfo/Africa/Banjul
- share/zoneinfo/Africa/Bissau
- share/zoneinfo/Africa/Blantyre
- share/zoneinfo/Africa/Brazzaville
- share/zoneinfo/Africa/Bujumbura
- share/zoneinfo/Africa/Cairo
- share/zoneinfo/Africa/Casablanca
- share/zoneinfo/Africa/Ceuta
- share/zoneinfo/Africa/Conakry
- share/zoneinfo/Africa/Dakar
- share/zoneinfo/Africa/Dar_es_Salaam
- share/zoneinfo/Africa/Djibouti
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- share/zoneinfo/Africa/Freetown
- share/zoneinfo/Africa/Gaborone
- share/zoneinfo/Africa/Harare
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- share/zoneinfo/Africa/Kampala
- share/zoneinfo/Africa/Khartoum
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- share/zoneinfo/Africa/Kinshasa
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- share/zoneinfo/Africa/Libreville
- share/zoneinfo/Africa/Lome
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- share/zoneinfo/Africa/Lubumbashi
- share/zoneinfo/Africa/Lusaka
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- share/zoneinfo/Africa/Mbabane
- share/zoneinfo/Africa/Mogadishu
- share/zoneinfo/Africa/Monrovia
- share/zoneinfo/Africa/Nairobi
- share/zoneinfo/Africa/Ndjamena
- share/zoneinfo/Africa/Niamey
- share/zoneinfo/Africa/Nouakchott
- share/zoneinfo/Africa/Ouagadougou
- share/zoneinfo/Africa/Porto-Novo
- share/zoneinfo/Africa/Sao_Tome
- share/zoneinfo/Africa/Timbuktu
- share/zoneinfo/Africa/Tripoli
- share/zoneinfo/Africa/Tunis
- share/zoneinfo/Africa/Windhoek
- share/zoneinfo/America/Adak
- share/zoneinfo/America/Anchorage
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- share/zoneinfo/America/Antigua
- share/zoneinfo/America/Araguaina
- share/zoneinfo/America/Argentina/Buenos_Aires
- share/zoneinfo/America/Argentina/Catamarca
- share/zoneinfo/America/Argentina/ComodRivadavia
- share/zoneinfo/America/Argentina/Cordoba
- share/zoneinfo/America/Argentina/Jujuy
- share/zoneinfo/America/Argentina/La_Rioja
- share/zoneinfo/America/Argentina/Mendoza
- share/zoneinfo/America/Argentina/Rio_Gallegos
- share/zoneinfo/America/Argentina/Salta
- share/zoneinfo/America/Argentina/San_Juan
- share/zoneinfo/America/Argentina/San_Luis
- share/zoneinfo/America/Argentina/Tucuman
- share/zoneinfo/America/Argentina/Ushuaia
- share/zoneinfo/America/Aruba
- share/zoneinfo/America/Asuncion
- share/zoneinfo/America/Atikokan
- share/zoneinfo/America/Atka
- share/zoneinfo/America/Bahia
- share/zoneinfo/America/Bahia_Banderas
- share/zoneinfo/America/Barbados
- share/zoneinfo/America/Belem
- share/zoneinfo/America/Belize
- share/zoneinfo/America/Blanc-Sablon
- share/zoneinfo/America/Boa_Vista
- share/zoneinfo/America/Bogota
- share/zoneinfo/America/Boise
- share/zoneinfo/America/Buenos_Aires
- share/zoneinfo/America/Cambridge_Bay
- share/zoneinfo/America/Campo_Grande
- share/zoneinfo/America/Cancun
- share/zoneinfo/America/Caracas
- share/zoneinfo/America/Catamarca
- share/zoneinfo/America/Cayenne
- share/zoneinfo/America/Cayman
- share/zoneinfo/America/Chicago
- share/zoneinfo/America/Chihuahua
- share/zoneinfo/America/Ciudad_Juarez
- share/zoneinfo/America/Coral_Harbour
- share/zoneinfo/America/Cordoba
- share/zoneinfo/America/Costa_Rica
- share/zoneinfo/America/Creston
- share/zoneinfo/America/Cuiaba
- share/zoneinfo/America/Curacao
- share/zoneinfo/America/Danmarkshavn
- share/zoneinfo/A
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warning libmamba [libgomp-14.2.0-h77fa898_1] The following files were already present in the environment:
- lib/libgomp.so
- lib/libgomp.so.1.0.0
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION.gomp_copy
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warning libmamba [_openmp_mutex-4.5-2_gnu] The following files were already present in the environment:
- lib/libgomp.so.1
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warning libmamba [libgcc-14.2.0-h77fa898_1] The following files were already present in the environment:
- lib/libatomic.so
- lib/libatomic.so.1
- lib/libatomic.so.1.2.0
- lib/libgcc_s.so
- lib/libgcc_s.so.1
- lib/libitm.so
- lib/libitm.so.1
- lib/libitm.so.1.0.0
- lib/libquadmath.so
- lib/libquadmath.so.0
- lib/libquadmath.so.0.0.0
- share/info/libgomp.info
- share/info/libquadmath.info
- share/licenses/gcc-libs/RUNTIME.LIBRARY.EXCEPTION
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warning libmamba [c-ares-1.34.4-hb9d3cd8_0] The following files were already present in the environment:
- bin/adig
- bin/ahost
- include/ares.h
- include/ares_build.h
- include/ares_dns.h
- include/ares_dns_record.h
- include/ares_nameser.h
- include/ares_version.h
- lib/cmake/c-ares/c-ares-config-version.cmake
- lib/cmake/c-ares/c-ares-config.cmake
- lib/cmake/c-ares/c-ares-targets-release.cmake
- lib/cmake/c-ares/c-ares-targets.cmake
- lib/libcares.so
- lib/libcares.so.2
- lib/libcares.so.2.19.3
- lib/pkgconfig/libcares.pc
- share/man/man1/adig.1
- share/man/man1/ahost.1
- share/man/man3/ares_cancel.3
- share/man/man3/ares_create_query.3
- share/man/man3/ares_destroy.3
- share/man/man3/ares_destroy_options.3
- share/man/man3/ares_dns_class_fromstr.3
- share/man/man3/ares_dns_class_t.3
- share/man/man3/ares_dns_class_tostr.3
- share/man/man3/ares_dns_datatype_t.3
- share/man/man3/ares_dns_flags_t.3
- share/man/man3/ares_dns_mapping.3
- share/man/man3/ares_dns_opcode_t.3
- share/man/man3/ares_dns_opcode_tostr.3
- share/man/man3/ares_dns_opt_datatype_t.3
- share/man/man3/ares_dns_opt_get_datatype.3
- share/man/man3/ares_dns_opt_get_name.3
- share/man/man3/ares_dns_parse.3
- share/man/man3/ares_dns_rcode_t.3
- share/man/man3/ares_dns_rcode_tostr.3
- share/man/man3/ares_dns_rec_type_fromstr.3
- share/man/man3/ares_dns_rec_type_t.3
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- share/man/man3/ares_dns_record.3
- share/man/man3/ares_dns_record_create.3
- share/man/man3/ares_dns_record_destroy.3
- share/man/man3/ares_dns_record_duplicate.3
- share/man/man3/ares_dns_record_get_flags.3
- share/man/man3/ares_dns_record_get_id.3
- share/man/man3/ares_dns_record_get_opcode.3
- share/man/man3/ares_dns_record_get_rcode.3
- share/man/man3/ares_dns_record_query_add.3
- share/man/man3/ares_dns_record_query_cnt.3
- share/man/man3/ares_dns_record_query_get.3
- share/man/man3/ares_dns_record_query_set_name.3
- share/man/man3/ares_dns_record_query_set_type.3
- share/man/man3/ares_dns_record_rr_add.3
- share/man/man3/ares_dns_record_rr_cnt.3
- share/man/man3/ares_dns_record_rr_del.3
- share/man/man3/ares_dns_record_rr_get.3
- share/man/man3/ares_dns_record_rr_get_const.3
- share/man/man3/ares_dns_record_set_id.3
- share/man/man3/ares_dns_rr.3
- share/man/man3/ares_dns_rr_add_abin.3
- share/man/man3/ares_dns_rr_del_abin.3
- share/man/man3/ares_dns_rr_del_opt_byid.3
- share/man/man3/ares_dns_rr_get_abin.3
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- share/man/man3/ares_dns_rr_get_addr.3
- share/man/man3/ares_dns_rr_get_addr6.3
- share/man/man3/ares_dns_rr_get_bin.3
- share/man/man3/ares_dns_rr_get_class.3
- share/man/man3/ares_dns_rr_get_keys.3
- share/man/man3/ares_dns_rr_get_name.3
- share/man/man3/ares_dns_rr_get_opt.3
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- share/man/man3/ares_dns_rr_key_datatype.3
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- share/man/man3/ares_dns_rr_set_addr6.3
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- share/man/man3/ares_dns_rr_set_u8.3
- share/man/man3/ares_dns_section_t.3
- share/man/man3/ares_dns_section_tostr.3
- share/man/man3/ares_dns_write.3
- share/man/man3/ares_dup.3
- share/man/man3
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warning libmamba [libexpat-2.6.4-h5888daf_0] The following files were already present in the environment:
- lib/libexpat.so.1
- lib/libexpat.so.1.10.0
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