From 71528a24e09abf1e77a7756db38490d892b4603f Mon Sep 17 00:00:00 2001 From: flu0r1ne Date: Mon, 31 Oct 2022 08:29:39 -0500 Subject: Fix readme --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index ff14ab3..c789e09 100644 --- a/README.md +++ b/README.md @@ -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) -- cgit v1.2.3