Update README

README.md

@@ -1,12 +1,23 @@
 # STELLAR3 - the SwifT Exact LocaL AligneR
-This is similar to [STELLAR](https://github.com/seqan/seqan/tree/master/apps/stellar) but adapted for seqan3 usage and
-added new cool features.
+This is similar to [STELLAR](https://github.com/seqan/seqan/tree/master/apps/stellar) but uses the [sharg parser](https://docs.seqan.de/seqan3/3-master-user/tutorial_argument_parser.html) and can be used to narrow the search to only a segment of the reference database.
 
-
-Instructions:
+## Building Stellar3:
 1. clone this repository: `git clone --recurse-submodules https://github.com/seqan/stellar3`
 2. create a build directory and visit it: `mkdir stellar3/build && cd $_`
 3. run cmake: `cmake ..`
 4. build the application: `make`
-5. optional: build and run the tests: `make test`
-6. execute the app: `./bin/stellar --help`
+5. show the help page: `./bin/stellar --help`
+
+## Running Stellar3:
+The `example` folder contains example data for a test run. Stellar3 can be used to produce soft-clipped read alignments or to find all local alignments between two genomes.
+
+Searching the reference sequences for local alignments with a minimum length of 50 and a maximum error rate of 0.02:
+`./bin/stellar -e 0.02 -l 50 -o mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`
+
+Searching only a segment of the reference for local alignments:
+`./bin/stellar --sequenceOfInterest 0 --segmentBegin 5000 --segmentEnd 7500 -e 0.02 -l 50 -o segment.mapped.reads.gff ../example/NC_001477.fasta ../example/reads.fasta`
+
+Finding all local alignments between two related genomes:
+`./bin/stellar -e 0.1 -l 50 -o alignments.gff ../example/NC_001474.fasta ../example/NC_001477.fasta`
+
+See the original [documentation](https://github.com/seqan/seqan/tree/main/apps/stellar) for details on the Stellar output formats.

example/alignments.gff

@@ -0,0 +1,14 @@
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	10542	10723	90.3225	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=10553,10735;eValue=2.35373e-61;cigar=30M1D5M1I22M1D7M1I1M1I50M1D2M1I62M;mutations=10C,11A,13C,16G,17G,27C,28C,32G,36T,66C,68C,74C,97G,121A,149A
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	10558	10723	91.7647	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=10570,10735;eValue=2.74788e-59;cigar=1D15M1D3M1I28M1I1M1D1M1I50M1D2M1I62M;mutations=10C,11C,14G,19T,48G,51C,57C,80G,104A,132A
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	9601	9710	90.09	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=9602,9711;eValue=1.90335e-33;cigar=78M1D1M1I30M;mutations=10T,12G,28G,30A,33A,44C,45G,62A,80A,90T
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	10290	10384	90.625	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=10311,10405;eValue=8.52734e-29;cigar=79M1D4M1I11M;mutations=10A,21C,37C,42T,45G,47G,55G,84T
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	10441	10520	90	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=10456,10534;eValue=4.46015e-22;cigar=9M1D70M;mutations=9C,19T,20G,46G,51C,52A,59T
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	43	121	90	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=42,118;eValue=4.46015e-22;cigar=3M1I4M1D26M1D43M1D;mutations=4A,8T,12T,59C,75A
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	3093	3157	90.7692	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=3091,3155;eValue=1.99822e-17;cigar=65M;mutations=13C,19T,22A,37C,40G,58C
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	5419	5477	90	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=5420,5478;eValue=7.66823e-15;cigar=16M1D1M1I41M;mutations=9C,18T,27A,35C,42C
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	9046	9101	91.0714	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=9047,9102;eValue=2.52061e-14;cigar=56M;mutations=19A,20G,30T,33A,36C
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	3400	3452	90.566	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=3398,3450;eValue=8.95234e-13;cigar=53M;mutations=3C,18C,34G,36C,45G
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	7785	7835	90.3846	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=7789,7839;eValue=2.94271e-12;cigar=15M1I1M1D34M;mutations=16C,19A,34A,40T
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	131	180	90.196	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=129,178;eValue=9.67292e-12;cigar=42M1I3M1D4M;mutations=22C,38A,43T,45T
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	7066	7115	90	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=7070,7118;eValue=3.17957e-11;cigar=45M1D4M;mutations=10A,12A,27A,36A
+gi|158976983|ref|NC_001474.2|	Stellar	eps-matches	8989	9038	90.196	+	.	gi|9626685|ref|NC_001477.1|;seq2Range=8990,9039;eValue=9.67292e-12;cigar=15M1D2M1I32M;mutations=18G,24G,30T,48T

example/mapped_reads.gff

@@ -0,0 +1,7 @@
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	10580	10629	98.0392	+	.	read01;seq2Range=24,74;eValue=4.77542e-20;cigar=19M1I31M;mutations=20C
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	6870	6923	98.1818	+	.	read03;seq2Range=46,100;eValue=4.09044e-22;cigar=29M1I25M;mutations=30C
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	6418	6519	98.0392	+	.	read04;seq2Range=1,100;eValue=7.44922e-45;cigar=76M1D24M1D;mutations=
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	9160	9222	98.4126	+	.	read08;seq2Range=11,73;eValue=3.00114e-26;cigar=63M;mutations=52N
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	7149	7217	98.5507	+	.	read10;seq2Range=1,69;eValue=2.37916e-29;cigar=69M;mutations=48A
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	9870	9939	98.5915	-	.	read02;seq2Range=1,71;eValue=2.20193e-30;cigar=20M1I50M;mutations=21C
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	9056	9151	98.9583	-	.	read06;seq2Range=6,100;eValue=2.64571e-43;cigar=2M1D93M;mutations=

example/segment.mapped.reads.gff

@@ -0,0 +1,3 @@
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	6870	6923	98.1818	+	.	read03;seq2Range=46,100;eValue=4.09044e-22;cigar=29M1I25M;mutations=30C
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	6418	6519	98.0392	+	.	read04;seq2Range=1,100;eValue=7.44922e-45;cigar=76M1D24M1D;mutations=
+gi|9626685|ref|NC_001477.1|	Stellar	eps-matches	7149	7217	98.5507	+	.	read10;seq2Range=1,69;eValue=2.37916e-29;cigar=69M;mutations=48A