2024/10/24-10:00:55 (Linux cray unknown)

README.md

@@ -8,3 +8,42 @@ The library excels in computing coverage tracks, summarizing sequence alignments
 One of the library's core strengths is its efficient handling of genomic ranges. It offers a highly optimized data structure for manipulating large genomic intervals, ensuring that operations like querying, merging, or intersecting genomic regions are performed with minimal overhead. Moreover, the library provides a pretty print feature for easily displaying genomic ranges in human-readable formats, facilitating better visualization and interpretation of complex data.
 
 Designed with performance and usability in mind, this library is ideal for large-scale genomics projects requiring both speed and precision, whether for research in genomics, epigenetics, or other related fields.
+
+## Documentation
+
+Please find the API documentation [here](https://docs.rs/rustynetics/latest/rustynetics/).
+
+## Examples
+
+### Read a BAM file into a GRanges object
+
+```rust
+use crate::bam::BamReaderOptions;
+use crate::granges::GRanges;
+
+let mut granges = GRanges::default();
+let mut options = BamReaderOptions::default();
+
+options.read_cigar = true;
+options.read_qual  = true;
+
+if Ok(_) = granges.import_bam_single_end("tests/test_bam_2.bam", Some(options)) {
+    println!("{}", granges);
+}
+```
+
+The result is:
+```bash
+     seqnames     ranges                 strand | flag mapq cigar                                                qual
+   1 chr15        [ 25969791,  25969842) +      |   99   60   51M @@@DFFFFHHHHGBHIBHHHGGGIHIEEHEIIIIIIGCHGHIGIGIIIIHH
+   2 chr15        [ 25969837,  25969888) -      |  147   60   51M GJJIIIIHIHDIHIIHHEGEEGJIIHFHIHCIHHGEIDHHDDHFDFFD@C@
+   3 chr1         [175925088, 175925139) -      |  153    0   51M IIIIIJJJIJJJJJJJJIJGIJIJHJJJJJJJIIJJJJHHHHHFFFFFBCC
+   4 chrX         [ 71582197,  71582248) -      |   83   60   51M GGDDIIIGJIJJJJJJJJJHGEHGJJJJIHDEIIGIJJGHHFHFFFFFCC@
+   5 chrX         [ 71581965,  71582016) +      |  163   60   51M @CCFFDFFHHDHHJJJIGCHGIGIGIGJJJIGCGCHBFGDBFGFGIJIJGC
+     ...          ...                           |  ...  ...   ...                                                 ...
+4887 chr11        [  9074777,   9074828) +      |  163   29   51M <@:B;DDDFH:CC>CFEAADFFFCDFHIEHIHJEGGEHIJJIIDGGIGHII
+4888 chr7         [  3303179,   3303230) -      |   83   60   51M HIHH@GIIHGHGHCJHGJIIIIIJJJJIJJIIIIIIJJHHGHHFFFFFCCC
+4889 chr7         [  3303050,   3303101) +      |  163   60   51M <@<DADADAAFFFC@>DGEHIICEGH@HCCEGHCCEBGGGFG:BFCGGGBB
+4890 chr11        [  4737838,   4737889) -      |   83   60   51M DB9;HCD?D??:?:):)CCA<C2:@HFAHEEHF@<?<?:ACADB;:BB1@?
+4891 chr11        [  4737786,   4737837) +      |  163   60   51M @@<DDBDDFD+C?A:1CFDHBFHC<?F9+CGGI:49CCGFACE99?DC990
+```