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-rw-r--r--README.md12
1 files changed, 6 insertions, 6 deletions
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@@ -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)