I want to save my fastq files as CRAM files to save space. However, I do want to be able to get the reads back that I have in my fastq, in case I have to reallign in a different way in the future. Below I have the code that I use to do the conversions to BAM and back again. However, when I then check the number of lines in the original fastq with the converted fastq, the original is much smaller:

original: 17460203 (lines)
converted: 147610328 (lines)

The flagstat of the BAM file gives 71038660 + 2766504 in total (QC-passed reads + QC-failed reads) reads. I don't understand why the newly made has more reads, unless the conversion from BAM to fastq also adds reads that map on multiple locations as multiple reads. Should I remove all duplicated reads and then convert?

# align with STAR
STAR --readFilesIn fastq1.fq fastq2.fq \
          --genomeDir Gencode_human/ \
          --outFileNamePrefix example.

# fix mates with picard
java -jar $EBROOTPICARD/FixMateInformation.jar \
             INPUT=example.bam \
             OUTPUT=example.fixmates.bam \
             VALIDATION_STRINGENCY=LENIENT \
             CREATE_INDEX=true \
             SORT_ORDER=coordinate


# convert to cram with scramble from io_lib
scramble \
  -I bam \
  -O cram \
  -r Gencode_human/GRCh38.p5.genome.fa \
  example.fixmates.bam \
  example.cram 

# convert back to bam 
scramble \
   -I cram \
  -O bam \
  -m \
  -r Gencode_human/GRCh38.p5.genome.fa \
  example.cram \
  example.bam 

#sort by name
  samtools sort \
    -n \
    -o example.sorted.bam \
     example.bam 

#convert to fastq
samtools fastq \
  -@ 4 \
  -1 converted.fastq1.fq \
  -2 converted.fastq2.fq \
  example.sorted.bam