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| -rw-r--r-- | README.md | 12 |
1 files changed, 6 insertions, 6 deletions
@@ -3,19 +3,19 @@ Bam Query Index (qidx) > Warning: this is a work in progress -`qidx` is tool for indexing BAM alignments by query name. While the -samtools have the ability to sort data by query name (also called -the read name), there htslib does not provide built-in utilities +`qidx` is tool for indexing BAM alignments by query name. While +`samtools` have the ability to sort data by query name (also called +the read name), htslib does not provide built-in utilities to retrieve alignments by query name. This can be advantageous for examining multi-mapped alignments. -While a utility [bri](https://github.com/jts/bri) predated `qidx` -providing the same utilities, it reads all alignments into memory +A utility [bri](https://github.com/jts/bri) predated `qidx` and also +indexes BAM files by query name. Yet, it reads all alignments into memory which is impractical for most human genome data. Notes: -- `qidx` creates a disk-backed using a sparse memory-mapped file. The underlying +- `qidx` creates a disk-backed hashset using a sparse memory-mapped file. The underlying 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) |