cannot specify single read for casava fastq import #2307
Description
Are you using the latest version of samtools and HTSlib? If not, please specify.
(run samtools --version)
$ samtools --version
samtools 1.22.1
Using htslib 1.22.1
Copyright (C) 2025 Genome Research Ltd.
Samtools compilation details:
Features: build=configure curses=yes
CC: gcc
CPPFLAGS:
CFLAGS: -Wall -g -O2
LDFLAGS:
HTSDIR: /tmp/htslib-1.22.1
LIBS:
CURSES_LIB: -lncurses
HTSlib compilation details:
Features: build=configure libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes plugins=yes plugin-path=/usr/local/libexec/htslib: htscodecs=1.6.4
CC: gcc
CPPFLAGS:
CFLAGS: -Wall -g -O2 -fvisibility=hidden
LDFLAGS: -fvisibility=hidden -rdynamic
HTSlib URL scheme handlers present:
built-in: file, preload, data
S3 Multipart Upload: s3w+https, s3w+http, s3w
Amazon S3: s3+https, s3, s3+http
mmap: mmap
libcurl: rtmp, smtp, ldaps, rtsp, smb, tftp, pop3, smbs, imaps, pop3s, ftps, https, ftp, gopher, imap, http, ldap, smtps, dict, telnet
iRODS: irods, irods4.2.11
Google Cloud Storage: gs+http, gs+https, gs
crypt4gh-needed: crypt4gh
mem: mem
Please describe your environment.
- OS (run
uname -sron Linux/Mac OS orwmic os get Caption, Versionon Windows) - machine architecture (run
uname -mon Linux/Mac OS orwmic os get OSArchitectureon Windows) - compiler (run
gcc --versionorclang --version)
$ uname -sr
Linux 5.15.0-141-generic
$ uname -m
x86_64
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
I cannot import casava like single read fastq to fill the BC tag and get the FLAGS correct.
correct but missing BC as no -i flag used
$ samtools import -0 - <<EOF
@AV244103:NT1856569G:2447682535:2:10601:0548:0004 1:N:0:TGTAGTAA+AACGTTAC
CGACCAATATCACGAAAAT
+
FKLLILLLMMMMMMMNNNN
@AV244103:NT1856569G:2447682535:2:10601:0573:0066 1:N:0:TGTAGTAA+AACGTTGC
ATCAAGCTCTTGGAAGAGA
+
FLLLLLLKMMMMMMMNNNN
EOF
@HD VN:1.6 SO:unsorted GO:query
@CO Reverse with: samtools fastq -0 unpaired.fastq
@PG ID:samtools PN:samtools VN:1.22.1 CL:/usr/local/bin/samtools import -0 -
AV244103:NT1856569G:2447682535:2:10601:0548:0004 4 * 0 0 * * 0 0 CGACCAATATCACGAAAAT FKLLILLLMMMMMMMNNNN
AV244103:NT1856569G:2447682535:2:10601:0573:0066 4 * 0 0 * * 0 0 ATCAAGCTCTTGGAAGAGA FLLLLLLKMMMMMMMNNNN
and
$ samtools import - <<EOF
@AV244103:NT1856569G:2447682535:2:10601:0548:0004 1:N:0:TGTAGTAA+AACGTTAC
CGACCAATATCACGAAAAT
+
FKLLILLLMMMMMMMNNNN
@AV244103:NT1856569G:2447682535:2:10601:0573:0066 1:N:0:TGTAGTAA+AACGTTGC
ATCAAGCTCTTGGAAGAGA
+
FLLLLLLKMMMMMMMNNNN
EOF
@HD VN:1.6 SO:unsorted GO:query
@CO Reverse with: samtools fastq -N -o paired.fastq
@PG ID:samtools PN:samtools VN:1.22.1 CL:/usr/local/bin/samtools import -
AV244103:NT1856569G:2447682535:2:10601:0548:0004 4 * 0 0 * * 0 0 CGACCAATATCACGAAAAT FKLLILLLMMMMMMMNNNN
AV244103:NT1856569G:2447682535:2:10601:0573:0066 4 * 0 0 * * 0 0 ATCAAGCTCTTGGAAGAGA FLLLLLLKMMMMMMMNNNN
incorrect flags but with BC from -i import
$ samtools import -i - <<EOF
@AV244103:NT1856569G:2447682535:2:10601:0548:0004 1:N:0:TGTAGTAA+AACGTTAC
CGACCAATATCACGAAAAT
+
FKLLILLLMMMMMMMNNNN
@AV244103:NT1856569G:2447682535:2:10601:0573:0066 1:N:0:TGTAGTAA+AACGTTGC
ATCAAGCTCTTGGAAGAGA
+
FLLLLLLKMMMMMMMNNNN
EOF
@HD VN:1.6 SO:unsorted GO:query
@CO Reverse with: samtools fastq -N -o paired.fastq
@PG ID:samtools PN:samtools VN:1.22.1 CL:/usr/local/bin/samtools import -i -
AV244103:NT1856569G:2447682535:2:10601:0548:0004 77 * 0 0 * * 0 0 CGACCAATATCACGAAAAT FKLLILLLMMMMMMMNNNN BC:Z:TGTAGTAA+AACGTTAC
AV244103:NT1856569G:2447682535:2:10601:0573:0066 77 * 0 0 * * 0 0 ATCAAGCTCTTGGAAGAGA FLLLLLLKMMMMMMMNNNN BC:Z:TGTAGTAA+AACGTTGC
and even when specifying -0:
$ samtools import -i -0 - <<EOF
@AV244103:NT1856569G:2447682535:2:10601:0548:0004 1:N:0:TGTAGTAA+AACGTTAC
CGACCAATATCACGAAAAT
+
FKLLILLLMMMMMMMNNNN
@AV244103:NT1856569G:2447682535:2:10601:0573:0066 1:N:0:TGTAGTAA+AACGTTGC
ATCAAGCTCTTGGAAGAGA
+
FLLLLLLKMMMMMMMNNNN
EOF
@HD VN:1.6 SO:unsorted GO:query
@CO Reverse with: samtools fastq -0 unpaired.fastq
@PG ID:samtools PN:samtools VN:1.22.1 CL:/usr/local/bin/samtools import -i -0 -
AV244103:NT1856569G:2447682535:2:10601:0548:0004 77 * 0 0 * * 0 0 CGACCAATATCACGAAAAT FKLLILLLMMMMMMMNNNN BC:Z:TGTAGTAA+AACGTTAC
AV244103:NT1856569G:2447682535:2:10601:0573:0066 77 * 0 0 * * 0 0 ATCAAGCTCTTGGAAGAGA FLLLLLLKMMMMMMMNNNN BC:Z:TGTAGTAA+AACGTTGC
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