Are you using the latest version of samtools and [HTSlib]samtools
samtools 1.19.1
Please describe your environment.
Darwin 23.2.0
(using bioconda build of samtools, environment to reproduce can be created with
conda create -n samtools-1191 -c bioconda -c conda-forge samtools=1.19.1)
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
Using the command
samtools view -L bed.txt sam.txt
using the following files input files:
bed.txt
chrX 133551173 133551336
chrX 123220438 123220646
chr11 32417784 32418003
sam.txt
@HD VN:1.5 SO:coordinate
@SQ SN:chr11 LN:135006516
@SQ SN:chrX LN:155270560
VH00330:4:AAAGCGNM5:1:1203:10657:15502 147 chrX 123220531 60 29M1I121M = 123220410 -271 TCAGCAGCCGGGGGTCAACAGTACGGAGTAAAAAAATCAAAACCATCTACAGGAAAACGGAAAGTGGTTGAGGGCATGCAGCTTTCACTCAGTAAGGATATAATTTATTCTCTTTATATTTATCCCTAATGTTTACCAACTGAATTGTCAT ;CCC;CCCCCCCCCCCCCCCCCCCCCCCC;CC;CCC;CCCC;CC;CCCCCCCCCCCCCCCCCCCCC;CCCCCCCCCCCCCCCCC-CCCCCCCCCC;CCCCCCC-CCCCCCCCCC;CCCCCCCCCCCCCCCCCCCCCCCCC-CCCCC-CCCC NM:i:1 MD:Z:150 MC:Z:97M AS:i:143 XS:i:0 RG:Z:ATCCGTCTCAAGCTGAGG
samtools 1.19.1 outputs no reads while samtools 1.19.0 (and earlier) outputs one read.
Are you using the latest version of samtools and [HTSlib]samtools
samtools 1.19.1
Please describe your environment.
Darwin 23.2.0
(using bioconda build of samtools, environment to reproduce can be created with
conda create -n samtools-1191 -c bioconda -c conda-forge samtools=1.19.1)Please specify the steps taken to generate the issue, the command you are running and the relevant output.
Using the command
using the following files input files:
bed.txt
sam.txt
samtools 1.19.1 outputs no reads while samtools 1.19.0 (and earlier) outputs one read.