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authorflu0r1ne <flu0r1ne@flu0r1ne.net>2022-10-31 17:32:08 -0500
committerflu0r1ne <flu0r1ne@flu0r1ne.net>2022-10-31 17:32:08 -0500
commit6b28db8eb2d8a2761f8bde0dcfb9d5ceefe5827b (patch)
tree8a8e4adf1a9427498f09d717ed94adea3ae0c661
parent4cff48542cf04c92106f09d5ecf83bc6ff1d8354 (diff)
downloadqidx-6b28db8eb2d8a2761f8bde0dcfb9d5ceefe5827b.tar.xz
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@@ -15,8 +15,12 @@ which is impractical for most human genome data.
Notes:
+- Currently, `qidx` is very inefficient in terms of disk space. When indexing a 33GiB BAM file
+ (Illumina 35x), it takes up 22GiB on disk when using STD compression. It initially maps 1.2TiB
+ into memory. This is reduced to ~120GiB due to file holes. ZSTD block compression again reduces
+ this to 22GiB. When I get a chance, I hope to look into this further.
- `qidx` creates a disk-backed hashset using a sparse memory-mapped file. The underlying
-operating system must support `mmap` and file holes
+operating system must support `mmap` and file holes.
- `qidx` doesn't currently support compression. it is currently recommended to
-use block-level compression (such as `zfs` `zstd` compression)
-- the bamfile must be sorted by query name before the index is built `samtools sort -n`
+use block-level compression (such as `zfs` `zstd` compression.)
+- The bamfile must be sorted by query name before the index is built `samtools sort -n`.