Bamclipper topics migration#10882
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santiagotariza wants to merge 11 commits intonf-core:masterfrom
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Co-authored-by: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
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SPPearce
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Mar 18, 2026
| "MT192765.1.primerclipped.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| "BAMCLIPPER", | ||
| "samtools", | ||
| "samtools 1.12\nUsing htslib 1.12\nCopyright (C) 2021 Genome Research Ltd.\n\nSamtools compilation details:\n Features: build=configure curses=yes \n CC: /opt/conda/conda-bld/samtools_1616004847436/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1616004847436/work=/usr/local/src/conda/samtools-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib\n HTSDIR: \n LIBS: \n CURSES_LIB: -ltinfow -lncursesw\n\nHTSlib compilation details:\n Features: build=configure plugins=yes, plugin-path=/usr/local/libexec/htslib libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes htscodecs=1.0\n CC: /opt/conda/conda-bld/htslib_1615999655191/_build_env/bin/x86_64-conda-linux-gnu-cc\n CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /usr/local/include\n CFLAGS: -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /usr/local/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1615999655191/work=/usr/local/src/conda/htslib-1.12 -fdebug-prefix-map=/usr/local=/usr/local/src/conda-prefix -fvisibility=hidden\n LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -L/usr/local/lib -fvisibility=hidden -rdynamic\n\nHTSlib URL scheme handlers present:\n built-in:\t preload, data, file\n S3 Multipart Upload:\t s3w, s3w+https, s3w+http\n libcurl:\t imaps, pop3, gophers, http, smb, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, mqtt, https, smbs, tftp, pop3s, dict\n Google Cloud Storage:\t gs+http, gs+https, gs\n Amazon S3:\t s3+https, s3+http, s3\n crypt4gh-needed:\t crypt4gh\n mem:\t mem" |
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We only want to capture 1.12 here.
This is such an old version of samtools, that maybe you'll need a different command?
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Closes #10218