add swifr module

packages/swifr/.gitignore

@@ -0,0 +1,4 @@
+bin
+./bin/*
+./external/*
+

packages/swifr/Makefile

@@ -0,0 +1,32 @@
+CC=g++
+CPPFLAGS=-std=c++11 -O3 -w
+CPPFLAGS2=-std=c++0x
+BIN=bin
+SRC=src/main.cpp
+
+TESTSRC=tests/*.cpp
+# include directories -- where to search for header files
+# include for tclap, io-lib, etc...
+
+INC=-I include/ -I /home/dannebar/software_downloads/io_lib-1.14.6/ -I ./external/io_lib_wrapper/ -I ./external/tclap-1.2.1/include/ 
+# lib directories -- whereto search for compiled static/dynamic libraries
+LIB=-L /home/dannebar/software_downloads/io_lib-1.14.6/lib
+IOLIBSO=$(BIN)/
+# io_tools for operating on the bams/sams
+# LIBS=lstaden-read
+EXE=swifr
+
+all: $(EXE) test
+
+$(EXE):
+	if [ ! -e $(BIN) ]; then mkdir $(BIN); fi
+	$(CC) $(CPPFLAGS) $(INC) $(LIB) -o $(BIN)/$@ $(SRC) -lstaden-read -lpthread -Wl,-rpath,"/home/dannebar/software_downloads/io_lib-1.14.6/lib/"
+
+
+test:
+	 $(CC) $(CPPFLAGS) $(INC) $(LIB) -o $(BIN)/$@ $(TESTSRC) -lstaden-read -Wl,-rpath,"/home/dannebar/software_downloads/io_lib-1.14.6/lib/" 
+
+clean:
+	rm $(BIN)/$(EXE)
+	# remove generated test files
+

packages/swifr/README.md

@@ -0,0 +1,55 @@
+# SWIFR: Smith-Waterman Implementation for Full Read-identifaction.
+
+SWIFR utilizes the Smith Waterman algorithm to align a set of query sequences against ngs reads
+
+### Manual
+
+Read the [Manual](manual/Manual.md) to learn about the command line parameters.
+The [Alignment Strategy](manual/AlignmentStrategy.md) is also useful for understanding the alignment method.
+
+### Dependencies
+
+* `io_lib_wrapper` - (provided in external/io_lib_wrapper )
+* `io_lib` - available at [SourceForge](http://sourceforge.net/projects/staden/files/io_lib/1.14.6/io_lib-1.14.6.tar.gz/download)
+* `kseq.h` - For reading Fasta files
+* `tclap` - Command Line Parsing available at [SourceForge](https://sourceforge.net/projects/tclap/files/tclap-1.2.1.tar.gz/download)
+
+
+##### Installing io_lib
+
+```
+wget [link above] && tar -xvzf [io_lib-1.14.6.tar.gz]
+./configure
+make
+make install
+```
+
+You may need to provide CCPFLAGS (additional directories to search for header) and CC (which compiler) variables to the configure:
+
+```
+./configure CPPFLAGS="-I /usr/local/include/" CC="gcc"
+```
+
+If LZMA is missing, you can install XZ utils with `homebrew install xz`.
+
+##### Installing TCLAP
+
+```
+wget [link above] && tar -xvzf [tclap-1.2.1.tar.gz]
+./configure
+make
+make install
+```
+
+#### compile swifr:
+
+```
+make
+```
+
+### Example of how to run swifr
+
+```
+/path/to/bin/swifr -f reads.fastq -q query_seqs.fasta -p 20 -s 20 -m 1 -k 10,1
+```
+

packages/swifr/external/io_lib_wrapper/.gitignore

@@ -0,0 +1,5 @@
+*.bam
+*.bai
+*.sam
+*.sai
+

packages/swifr/external/io_lib_wrapper/Makefile

@@ -0,0 +1,40 @@
+# compile examples
+CC=g++
+# CPPFLAGS=-std=c++11 -O3 -w
+# quick compilation
+CPPFLAGS=-std=c++11 -w
+SRC=examples
+TESTSRC=tests/test_*.cpp
+BIN=.
+INC=-I . -I /usr/local/include/
+TESTINCLUDE=-I io_lib_wrapper -I tests
+LIB=-L /usr/local/lib/
+# io_tools for operating on the bams/sams
+# LIBS=lstaden-read
+
+all: create reading_bam writing_bam reading_fasta reading_reference_fasta test
+
+create:
+	if [ ! -e $(BIN) ]; then mkdir $(BIN); fi
+
+reading_bam:
+	$(CC) $(CPPFLAGS) $(INC) $(LIB) -o $(BIN)/$@ $(SRC)/reading_bam.cpp -lstaden-read
+
+writing_bam:
+	$(CC) $(CPPFLAGS) $(INC) $(LIB) -o $(BIN)/$@ $(SRC)/writing_bam.cpp -lstaden-read
+
+reading_fasta:
+	$(CC) $(CPPFLAGS) $(INC) $(LIB) -o $(BIN)/$@ $(SRC)/reading_fasta.cpp -lstaden-read
+
+reading_reference_fasta:
+	$(CC) $(CPPFLAGS) $(INC) $(LIB) -o $(BIN)/$@ $(SRC)/reading_reference_fasta.cpp -lstaden-read
+
+# compile tests
+test:
+	$(CC) $(CPPFLAGS) $(INC) $(TESTINCLUDE) $(LIB) -o $(BIN)/$@ $(TESTSRC) -lstaden-read
+
+clean:
+	# remove examples, testing binary
+	rm -f $(BIN)/test $(BIN)/reading_bam $(BIN)/writing_bam $(BIN)/reading_fasta $(BIN)/reading_reference_fasta
+	rm *.sam
+	rm *.bam	

packages/swifr/external/io_lib_wrapper/README.md

@@ -0,0 +1,54 @@
+# io_lib_wrapper
+
+This is a header-only wrapper around `io_lib` library that will help you interact with `io_lib` without having to understand their complex API.
+
+## Dependencies
+
+#### Staden io_lib
+
+`staden_io_lib` -- download the library from [SourceForge](http://sourceforge.net/projects/staden/files/io_lib/1.14.6/io_lib-1.14.6.tar.gz), unpack and follow the installation instructions:
+
+```
+wget [link above] && tar -xvzf [io_lib-1.14.6.tar.gz]
+./configure CPPFLAGS="-I /usr/local/include/" CC="gcc"
+make
+make install
+```
+
+You may need to provide CCPFLAGS (additional directories to search for header) and CC (which compiler) variables to the configure (as shown above).
+
+#### LZMA
+
+Install LZMA through XZ utils:
+
+```
+homebrew install xz
+```
+
+#### TCLAP
+
+C++ templatized header-only command line [parser](http://tclap.sourceforge.net/)
+
+## How to use
+
+#### Including in your projects
+
+This library is header-only, so you can simply place it next to your include folder
+and you are ready to go:
+
+  `src/` -- your main and other *.cpp files
+
+  `include/` -- your headers
+
+  `io_lib_wrapper/` -- io_lib_wrapper
+
+#### Reading a BAM file
+
+```
+  shared_ptr<Alignment> alignment = bamReader.getNextAlignment();
+	while ( alignment != nullptr ) {
+		alignment = bamReader.getNextAlignment();
+	}
+```
+
+You will find more runnable examples in `examples/`.

packages/swifr/external/io_lib_wrapper/bam/hxb2.fa

@@ -0,0 +1,141 @@
+>gi|1906382|gb|K03455.1|HIVHXB2CG Human immunodeficiency virus type 1 (HXB2), complete genome; HIV1/HTLV-III/LAV reference genome
+TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTA
+CTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTAC
+AAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACC
+CTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGC
+ATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAG
+GGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGAT
+CCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGC
+TCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTG
+TGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCT
+AGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCG
+GCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGC
+GGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAA
+AAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGC
+TAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCT
+ACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGT
+GTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAA
+GTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTAT
+AGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAA
+GTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCC
+CACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGAC
+CATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAG
+ATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGA
+CAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGT
+AAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTA
+GACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCT
+TGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGA
+AGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATG
+AGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTA
+AGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTG
+GAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATC
+TGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAG
+AGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTA
+TCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAA
+AGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAA
+ACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATC
+TGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGT
+TGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCC
+AGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATT
+TGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTAT
+TTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAAC
+TCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACA
+GTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTA
+CCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAA
+AGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAC
+ATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAA
+AAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGA
+ACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCA
+GAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTT
+ACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACC
+ACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTG
+TATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAA
+TTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGA
+TGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCT
+AAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGA
+TTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCAT
+AGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATAT
+GTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAG
+CAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGG
+AATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAA
+AAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAAT
+TAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAA
+ATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTA
+GCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATAT
+GGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATAT
+AGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGA
+TGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTT
+GGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTAT
+GAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAA
+ATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAG
+TAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCG
+GGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGG
+GCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATT
+ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTT
+TAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCC
+TCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGG
+GGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGAT
+ATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGA
+CTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAAC
+AAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGC
+CTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCA
+CACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTT
+GGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAAT
+AAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTAC
+TCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCA
+GCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACA
+AAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGA
+CTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGT
+AGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATA
+TTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGA
+GTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGA
+TGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAAC
+CACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACAT
+GCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGT
+GGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATG
+TGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGT
+AGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAA
+GAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTAC
+CAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCA
+ATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAA
+CAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACT
+GCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAA
+ACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAA
+GAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGC
+ACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAA
+TTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTT
+TTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTAC
+TTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAA
+ATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTT
+CATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAG
+ACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAA
+CCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAG
+GAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGT
+ACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAA
+CAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGAT
+ACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCC
+TTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGAC
+AGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGA
+ATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCT
+GTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTT
+TCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGG
+GACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGT
+GAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGA
+GACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATT
+GGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGC
+CATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCAC
+ATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGT
+AGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAG
+CAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTG
+TGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCA
+ATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTC
+ACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCA
+GAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTT
+GAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATG
+GGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGC
+CCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGG
+GACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAG
+CTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAG
+GGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTG
+TGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
+

packages/swifr/external/io_lib_wrapper/examples/reading_bam.cpp

@@ -0,0 +1,29 @@
+#include <iostream>
+#include <memory>
+#include <ctime>
+#include "io_lib_wrapper/bam_reader.hpp"
+#include "io_lib_wrapper/alignment.hpp"
+
+using namespace std;
+
+int main() {
+	clock_t start = std::clock();
+	string fname = "examples/test.bam";
+	BamReader bamReader(fname);
+	if (!bamReader.is_open()) {
+		exit(1);
+	}
+
+	int primary_alignments = 0;
+	shared_ptr<Alignment> alignment = bamReader.getNextAlignment();
+	while ( alignment != nullptr ) {
+		if (!alignment->is_unaligned() && alignment->is_primary() ) {
+			primary_alignments++;
+		}
+		alignment = bamReader.getNextAlignment();
+	}
+	cerr << "Read " << bamReader.getLineCount() << " alignments," 
+		" of them " << primary_alignments << " are unique best" << endl;
+	cerr << "Time to read: " << 
+		(std::clock() - start) / (double)(CLOCKS_PER_SEC / 1000) << "ms" << endl;
+}

packages/swifr/external/io_lib_wrapper/examples/reading_fasta.cpp

@@ -0,0 +1,9 @@
+#include <iostream>
+#include <memory>
+#include "io_lib_wrapper/fasta_reader.h"
+
+using namespace std;
+
+int main() {
+	cerr << "TODO" << endl;
+}

packages/swifr/external/io_lib_wrapper/examples/reading_reference_fasta.cpp

@@ -0,0 +1,7 @@
+#include <iostream>
+#include <memory>
+#include "io_lib_wrapper/long_sequence.hpp"
+
+int main() {
+	cerr << "TODO" << endl;
+}