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jts / bam2fastq

Simple convertor from bam to FASTQ
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not working here #3

Closed juancresc closed 5 years ago

juancresc commented 5 years ago

(base) ➜ lan-dic ./../sw/bam2fastq/bam2fastq -o data/landic_svevo_1.un.fastq data/landic_svevo_1.un.sam [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid [1] 19566 abort (core dumped) ./../sw/bam2fastq/bam2fastq -o data/landic_svevo_1.un.fastq

jts commented 5 years ago

You're tried to pass in a sam file. This program converts bam to fastq.