GzDecoder truncates multi-member gzip input: reads are silently dropped #217

Summary

Gzipped input is decoded with flate2::read::GzDecoder, which stops at the end of the first
gzip member. A multi-member .gz is therefore read partially, silently: no error, no warning,
just fewer reads. flate2::read::MultiGzDecoder is the variant that consumes concatenated members.

This matters in practice because multi-member gzip is normal in this domain: bcl2fastq output,
any cat a.fq.gz b.fq.gz > merged.fq.gz, and every BGZF file (BGZF is multi-member gzip).

Reproduction

On main, using only the fixtures bundled in the repo:

# 3 reads total, split across two gzip members
head -8 test/reads.fq | gzip -c  > /tmp/multi.fq.gz
tail -4 test/reads.fq | gzip -c >> /tmp/multi.fq.gz
# same 3 reads, one member
gzip -c test/reads.fq > /tmp/single.fq.gz

cargo run -- --runMode genomeGenerate --genomeDir /tmp/idx \
    --genomeFastaFiles test/simple.fa --genomeSAindexNbases 4
for f in single multi; do
  cargo run -- --genomeDir /tmp/idx --readFilesIn /tmp/$f.fq.gz \
      --outFileNamePrefix /tmp/out_$f/ --outSAMtype BAM SortedByCoordinate
  grep 'Number of input reads' /tmp/out_$f/Log.final.out
done

Both files decompress to the same 12 lines with gunzip/Python. The aligner sees one read fewer,
and exits 0.

Affected sites

All four read paths use the single-member decoder:

• src/io/fastq.rs:106 — FASTQ input (the one that matters most)
• src/solo/whitelist.rs:524 — barcode whitelist
• src/solo/count.rs:2090
• src/bin/emptydrops.rs:92

Fix

GzDecoder → MultiGzDecoder at those four sites. No API change, no new dependency; the type is
already in the flate2 version in the tree.

Suggested regression test

An integration test that builds a two-member .fq.gz from the bundled fixture and asserts the read
count matches the plain-text run. Cheap, and it locks the behaviour against a future refactor
picking the wrong decoder again.

Note

Detection is also extension-based today (path_str.ends_with(".gz"), src/io/fastq.rs:92), so a
compressed file with an unexpected name is read as plain text and a plain file named .gz fails.
That is a separate question, tracked with the multi-format input issue.