Hi!
When I try to use CRAM files as input, I got the following message:
Error in get_bam_name_and_maybe_convert_cram(iBam, bam_files, cram_files, :
Both bam_files and cram_files are empty
Calls: QUILT ... loadBamAndConvert -> get_bam_name_and_maybe_convert_cram
Execution halted
Hi! When I try to use CRAM files as input, I got the following message:
Error in get_bam_name_and_maybe_convert_cram(iBam, bam_files, cram_files, : Both bam_files and cram_files are empty Calls: QUILT ... loadBamAndConvert -> get_bam_name_and_maybe_convert_cram Execution halted
And when I convert CRAM files to BAM files, it can work. I notice that in https://github.com/rwdavies/QUILT/blob/master/QUILT/R/functions.R
loadBamAndConvert( iBam = iSample, L = L, pos = pos, nSNPs = nSNPs, bam_files = bam_files, iSizeUpperLimit = iSizeUpperLimit, bqFilter = bqFilter, chr = chr, N = length(sampleNames), downsampleToCov = downsampleToCov, sampleNames = sampleNames, inputdir = tempdir, regionName = regionName, tempdir = tempdir, chrStart = chrStart, chrEnd = chrEnd, chrLength = NA, save_sampleReadsInfo = TRUE, use_bx_tag = use_bx_tag, bxTagUpperLimit = bxTagUpperLimit, default_sample_no_read_behaviour = "return_null" )
there is no "cram_files = cram_files", is that a mistake? Thanks!