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It appears reads in tab5 format are processed when using --12 filename but not when read from stdin using --12 -.
--12 filename
--12 -
$ bowtie --version bowtie-align version 1.2 64-bit Built on ElCapitan.local Sun Feb 19 14:05:23 GMT 2017 Compiler: InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin Options: -O3 -m64 -stdlib=libstdc++ -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8} $ cat fragments.tab5 H06HDADXX130110:2:2116:3345:91806 GTTAGGGTTAGGGTTGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGCTAGGGTTAAGGGTAGGGTTAGCGAAAGGGCTGGGGTTAGGGGTGCGGGTACGCGTAGCATTAGGGCTAGAAGTAGGATCTGCAGTGCCTGACCGCGTCTGCGCGGCGACTGCCCAAAGCCTGGGGCCGACTCCAGGCTGAAGCTCAT >=<=???>?>???=??>>8<?>=2=<===1194<?;:?>>?#3==>########################################################################################################################################################################################################### TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCGTACCCTAAACCCAACCCTAACCACAAAGCAAATCCCAACCTTAACCGGAACCCGAAATCTCGCAGCAAATCTGCAGTAGAGACGCAGACTCAACCATGCGTCTATTAGTACGCATTATCATTGCCTCATGCTTCTTAAGTACAGAGAGATGAC ==;<?>@@@<>>@??<>>???<=>>?>:><@?4=:>7=5=>:=@;'@A?######################################################################################################################################################################################################## ... $ bowtie -S GCA_000001405.25_GRCh38.p10_genomic --12 fragments.tab5 @HD VN:1.0 SO:unsorted @SQ SN:CM000663.2 LN:248956422 ... @PG ID:Bowtie VN:1.2 CL:"bowtie-align --wrapper basic-0 -S GCA_000001405.25_GRCh38.p10_genomic --12 fragments.tab5" H06HDADXX130110:2:2116:3345:91806 77 * 0 0 * * 0 0 GTTAGGGTTAGGGTTGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGCTAGGGTTAAGGGTAGGGTTAGCGAAAGGGCTGGGGTTAGGGGTGCGGGTACGCGTAGCATTAGGGCTAGAAGTAGGATCTGCAGTGCCTGACCGCGTCTGCGCGGCGACTGCCCAAAGCCTGGGGCCGACTCCAGGCTGAAGCTCAT >=<=???>?>???=??>>8<?><=2=<===1194<?;:?>>?#3==>########################################################################################################################################################################################################### XM:i:0 H06HDADXX130110:2:2116:3345:91806 141 * 0 0 * * 0 0 TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCGTACCCTAAACCCAACCCTAACCACAAAGCAAATCCCAACCTTAACCGGAACCCGAAATCTCGCAGCAAATCTGCAGTAGAGACGCAGACTCAACCATGCGTCTATTAGTACGCATTATCATTGCCTCATGCTTCTTAAGTACAGAGAGATGAC ==;<?>@@@<>>@??<>>???<=>>?>:><@?4=:>7=5=>:<=@;'@A?######################################################################################################################################################################################################## XM:i:0 ... # reads processed: 4 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 4 (100.00%) No alignments $ cat fragments.tab5 | bowtie -S GCA_000001405.25_GRCh38.p10_genomic --12 - @HD VN:1.0 SO:unsorted @SQ SN:CM000663.2 LN:248956422 ... @PG ID:Bowtie VN:1.2 CL:"bowtie-align --wrapper basic-0 -S GCA_000001405.25_GRCh38.p10_genomic --12 -" # reads processed: 0 # reads with at least one reported alignment: 0 (0.00%) # reads that failed to align: 0 (0.00%) No alignments
The text was updated successfully, but these errors were encountered:
Fixed in Bowtie 1.2.1
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ch4rr0
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It appears reads in tab5 format are processed when using
--12 filename
but not when read from stdin using--12 -
.The text was updated successfully, but these errors were encountered: