missing test on the presence of the bai file in the same directory as the bam file
python3.6 scripts/intronSeeker.py split --input first_test_hisat2/first_test.Aligned.sortedByCoord.out.bam --reference data/Reduced_real_dataset/Test_set_Cele_contig-assembly.fasta -o first_test_hisat2b
Traceback (most recent call last):
File "scripts/intronSeeker.py", line 172, in
args.func(**param)
File "/media/Stock/src/intronSeeker-master/scripts/intronResearch.py", line 77, in split_research
res_gff,res_tmp = find_split(fastafilename,bamfilename) ;
File "/media/Stock/src/intronSeeker-master/scripts/intronResearch.py", line 112, in find_split
aligned = bamfile.fetch(id, multiple_iterators=True)
File "pysam/libcalignmentfile.pyx", line 1092, in pysam.libcalignmentfile.AlignmentFile.fetch
ValueError: fetch called on bamfile without index