Awesome
jbwa
Java Bindings (JNI) for bwa
Author: Pierre Lindenbaum PhD. @yokofakun (Institut du Thorax, Nantes, France) BWA is written by Heng Li (Broad Institute)
Motivation
BWA (http://bio-bwa.sourceforge.net/) contains a small C example(https://github.com/lh3/bwa/blob/master/example.c) for running bwa-mem as a library (bwamem-lite). I created some JNI bindings to see if I can bind the C bwa library to java and get the same output than bwamem-lite.
Compilation
I've tested this code under linux and
- JAVA oracle JDK8
- GNU Make 3.81
- gcc 4.8.2
- wget
BWA for apache2 will be downloaded ( https://github.com/lh3/bwa/tree/Apache2 ) .
typing make, should download the sources bwa, compile and execute some tests.
See also
Contribute
- Issue Tracker: http://github.com/lindenb/jbwa/issues
- Source Code: http://github.com/lindenb/jbwa
License
The project is licensed under the Apache2 license.
Example (Two FASTQs)
System.loadLibrary("bwajni");
//load the index
BwaIndex index=new BwaIndex(new File(args[0]));
//load the bwa engine
BwaMem mem=new BwaMem(index);
//get reads from two fastqs
KSeq kseq1=new KSeq(new File(args[1]));
KSeq kseq2=new KSeq(new File(args[2]));
//build a list of two fastqs, forward and reverse
List<ShortRead> L1=new ArrayList<ShortRead>();
List<ShortRead> L2=new ArrayList<ShortRead>();
//while something can be done
for(;;)
{
//read the pair of fastq
ShortRead read1=kseq1.next();
ShortRead read2=kseq2.next();
//should we analyze and dump the data ?
if(read1==null || read2==null || L1.size()>100)
{
if(!L1.isEmpty())
for(String sam:mem.align(L1,L2)) //get the SAM records
{
System.out.print(sam);
}
if(read1==null || read2==null) break;
L1.clear();
L2.clear();
}
L1.add(read1);
L2.add(read2);
}
kseq1.dispose();
kseq2.dispose();
index.close();
mem.dispose();
Testing
Here is the ouput of the JAVA version:
java -Djava.library.path=src/main/native -cp src/main/java com.github.lindenb.jbwa.jni.Example2 \
human_g1k_v37.fasta tmp1.fq tmp2.fq
HWI-1KL149:20:C1CU7ACXX:4:1101:13638:2192 121 1 229568362 37 13S87M = 229568362 0 GCTCTTCCGATCTGGCACGTTGAAGGTCTCAAACATGATCTGGGTCATCTTCTCGCGGTTGGCCTTGGGATTGAGGGGGGCCTCGGTGAGCAGGGNGGGG AB?DDDDDDDBDCDDDDDDDDDDCDDDDCCC>(DCDDDDDDBDDDCCCCBDDDFFEEJIHIJIIHJIJJJJJJIJJJJJJJJJJJJJHHHHHDA2#FCCC NM:i:1 AS:i:85 XS:i:61
HWI-1KL149:20:C1CU7ACXX:4:1101:13638:2192 181 1 229568362 0 * = 229568362 0 GCTCTTCCGATCTCCCCACCCTGCTCACCGAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGNNNNNNNNNNNNNNNNNNAACGTGCC ?DDDDDDDDDDDDDDB?9BDDDDDDDBBB?8,,######################################?12##################FFFFFCCC AS:i:0 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:1424:2423 69 X 16753128 0 * = 16753128 0 AGATNGGAAGAGCACACGTCTGAACTCCAGTCACCAAGGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACAAATACGGATGAGACATG CCCF#2ADHHHHHJJJJJJJJJJJJJJ>9:1*1C3C8D600)0*0*/00-.8B)--5B().).=).?CFFFBBBDB######################## AS:i:0 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:1424:2423 137 X 16753128 0 58S34M8S = 16753128 0 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAACAAAAAAAGAGATGAACAAGCAAA CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJHIHIIJJJJJJJHJJIIJJJHFFFFEEEEEEEDDDD################################## NM:i:0 AS:i:34 XS:i:29
HWI-1KL149:20:C1CU7ACXX:4:1101:2908:2463 97 12 110765491 60 70M30S = 110765491 70 AATTNGGGGAACAGCTTTCCAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATATTGGGCAAGATCGGAAGAGCACACGTCTGAACTCCAG CCCF#4BDHGHHHJJJJJJJJJIJHIJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJIIIIHIJJJJIIIJIJJGHEHFFFEDDEEAA@BDDDCDDDD:C@ NM:i:1 AS:i:68 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:2908:2463 145 12 110765491 60 30S70M = 110765491 -70 CTCTTTCCCTACACGACGCTCTTCCGATCTAATTTGGGGAACAGCTTTCCAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATATTGGGCA DDDDDDDDDCAB=DDBDEEFFFFHHHJJJGHHGGFJJJJJIIIIJJJJJIJJJJJIJIIIJJJJJJJJJJJJIJJHHHFHEEJJIJJHHHHHFFFFFCBC NM:i:0 AS:i:70 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:4663:2297 81 4 114279632 60 100M = 114279455 -277 GATTCCTACTGCACCCATGGAGAATGTGCCTTTTACTGAAAGCAAATCCAAAATTCCTGTAAGGACTATGCCCACTTCCACCCCAGCACCTCCATNTGCA DCDDDDCACCDBCBCDDDCDDCCA?EEDDDFFDFFFHHHGHHHJJJJJJJJIJJIJIJJIJIJJJJJJJJJJIGJJIIHFIJJJJHGDHHDHDA2#FCCB NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:4663:2297 161 4 114279455 60 100M = 114279632 277 CGTGCAAACGGGTGATATACCTCCTCTCTCTGGTGTAAAGCAGATATCCTGCCCCGACTCTTCTGAACCAGCTGTACAAGTCCAGTTAGATTTTTCCACA CCBFFFFFHHHHFHIJJJJJIIJJJJJJJJJJJHIGIJIIJJJJJJJJJJHIJJJJJJJHHHHHHFDDDFDDEEEDDDADCCDDDCCDCCDEDDDCACCC NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:6872:2320 81 2 179597667 60 100M = 179597628 -139 GGCTGTGCCTTCCACAAATGCTATCCTGTATCTGTCAGAAGCAGCTATTTCTTTGCCATCCTTAAACCAGGACACCCTCATGGGGAGGGAGCCTGNAATT ABDDDDDBDDDDDDEDDEDDDEECEEFFFFFFHGHHHHJJIJJJJJIIJJIJJJJJJJJJIIJIHGJJJJJHHEJJIHJJJJJJJJJHHHHHDA2#FCCC NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:6872:2320 161 2 179597628 60 100M = 179597667 139 CCCTGCATCATTCATGTCTACTCTGATGATCTCCAAAGAGGCTGTGCCTTCCACAAATGCTATCCTGTATCTGTCAGAAGCAGCTATTTCTTTGCCATCC CCCFFFFFHHHHHJJJJJJJJJJJJIJJJJJJJJJJJJJJIIJJIIHJJJJIJJGIIIJJJIIJIIIHGIJJJJJIIEHHHHHHFBFFDEFECDECCDDA NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:9215:2408 97 2 220283746 60 100M = 220283863 217 CAGCNGCTCAAGGCCAAGTGAGGGCCCGGCACCCCAGACTCCTCTTTCTGCGGGCAGGGCACAGGAGGCTAGGCCTGGGGGCTGGGGTCCCGCTGTCAGC CCCF#2ADHHHHHFIJIIHIGIJJJJJJJJIIJJJJIJJJJJJJIIIJJIGFFFDDDDDDDBDDD?BDBDCBBDDCDDDDDBDDDBB>BBDDDDB@CDCD NM:i:2 AS:i:93 XS:i:23
HWI-1KL149:20:C1CU7ACXX:4:1101:9215:2408 145 2 220283863 60 100M = 220283746 -217 GCCCGGGACCCTCTCCTGCCCCATGTGGAGAAAGGGTCCTCCACCTGTGTGTTTCAAGGGGCCGTGACCTCCAGGTCTCTCCCCCTGCGATCCCATCTTG BDDBDBC?DDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDCADDDDDBEEEEEFFFFHHIJJJIHGJJJIJJJJJIIIIJIJJJJJHHHGHFFFFFCCC NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:9815:2325 97 22 46114322 60 100M = 46114410 188 AAAGNCCGGAATTGGTACAAGCCATGTTTCCCAAACTGAACAATCAAGAAAGGTAACCCCCCAACCAGCGTGGTCTGGAGTATTTAGCATTCCATATAGG CCCF#2ADHHHHHJJGHIJJJJJJJJIGJJJJJJJJJJJJJJJJJJJJGHIJJHIJJIIJJHFFFFDDCD?BDDDCCDCD>ACDEEDDDEDDEDCCCCCD NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:9815:2325 145 22 46114410 60 100M = 46114322 -188 ATTCCATATAGGGTATTCGATGCACGTGACTGAAAAGCTGTGTGGTTTCTGAGTTGGCACAGAATCTCTAAATACATGTTTCTGTGTTGGTAATGGTTTT DDCDEDCCDDDDCDDEEDEFFFFFHHHHIJJJJJJJIJJJJIIJJJIIGGJJJJJIJJJJJJJJIIHJJJJJIIJJJJJJJIIJIJIHFHHHFFFFFCCC NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11401:2488 97 3 38763808 60 100M = 38763855 147 CCACNATACGGTAGCAAGTCTTGCGCACCTGCCAGCCCACATCCCATGGACTCTTCGTGGTATCCAGTTTGCAGCAGGGACAGTGGCGAATGCATCCTGT CCCF#4ADHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJEIJJIJJJHHHFFFFFFFEEEEEEEDABBDDDBBCCDBD>BDDDDEDDDD> NM:i:2 AS:i:93 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11401:2488 145 3 38763855 60 100M = 38763808 -147 GGACTCTTCGTGGTATCCAGTTTGCAGCAGGGACAGTGGCGAATGCATCCTGTGGGGAGAGGTGACTGATGGTGGGTGATGGCCAGTGGGCAAAGGGGAT DDCDDDB?DCCCDECDDCDDDCDDEEDEFFFFFFHHHJJIJJJIJIIJIJJJIJJIJJJJJJJJIJJJJJJJJJJIJJJJJJJJJJJHHHHHFFFFFCCC NM:i:1 AS:i:95 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11658:2375 97 7 35293037 60 100M = 35293129 192 CAGCNAGGGGCACAGACGGATGCGCAGCATCCCCAGTCCTCGGCGGACAGCCGGGTAGCCCAACTTACCCAGGGGTTTGATTGTGTTCTCCGTCGCCTCC CCCF#2ADHHHHHJIIJJJJIJJJJJJJJJIJJJJJIJJJJJJJJDDDDDDDDDDBBDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDCEDCB?ABDBDD1 NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11658:2375 145 7 35293129 60 100M = 35293037 -192 TCGCCTCCTTCTCCTTAGAGCCGCCGCTCGACATGAGCGCGGCAATGGAGAAGGCGTTGGCCCGGGAGGAGAGTTGGGGCTTGGGGGACGCCGTGAACTC DDBBBDDCA8DDDCC@DDDBDDDDDDDDDDEDDDDDDDDDDDDEDDDDCCDDDDFFFHHJJJJJJJJJHJJJJJJJJJJJJJJJJJJHHHHHFFFFDCBB NM:i:1 AS:i:95 XS:i:20
HWI-1KL149:20:C1CU7ACXX:4:1101:12054:2300 97 2 40401764 60 100M = 40401971 307 CAAGNTACATAAGATGTAGGTTTGGATTGATGGTTAAGGGTATTTGGGGAAAAATAAGGAACATTAAAAAAATAAGTCTTACCAAACAGGTATTTTCCTT CCCF#4=DHHHHHIJJHIJJHIJJJHIJJIIJJEGHJJJJDGIJJJJJJGHHIJJIIJJJIIIIJIJJHHFDEDECDDEEDDDDDDDDDDCCDEEEDDCD NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:12054:2300 145 2 40401971 60 100M = 40401764 -307 TTGTGAAGCCACCTAAAAAAGAAAAAAACAACAACAAATGTTATAATTTGACACTCTACATAACAAATACCAGTGACATCAGACTGCCTGACAACCCACC @CC@DDDDDDDDDDDDDDDDDDFHHHHEIIHIIIJJJIJJJJJJJJJIHDIJJJJJIIJJJJIJJJJHFJJJJJJIJJJJJJJJJJJHHHHHFFFFDBCB NM:i:0 AS:i:100 XS:i:0
And the ouput of the Native C version:
bwa mem human_g1k_v37.fasta tmp1.fq tmp2.fq 2> /dev/null | grep -v -E '^@'
HWI-1KL149:20:C1CU7ACXX:4:1101:13638:2192 121 1 229568362 37 13S87M = 229568362 0 GCTCTTCCGATCTGGCACGTTGAAGGTCTCAAACATGATCTGGGTCATCTTCTCGCGGTTGGCCTTGGGATTGAGGGGGGCCTCGGTGAGCAGGGNGGGG AB?DDDDDDDBDCDDDDDDDDDDCDDDDCCC>(DCDDDDDDBDDDCCCCBDDDFFEEJIHIJIIHJIJJJJJJIJJJJJJJJJJJJJHHHHHDA2#FCCC NM:i:1 AS:i:85 XS:i:61
HWI-1KL149:20:C1CU7ACXX:4:1101:13638:2192 181 1 229568362 0 * = 229568362 0 GCTCTTCCGATCTCCCCACCCTGCTCACCGAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGNNNNNNNNNNNNNNNNNNAACGTGCC ?DDDDDDDDDDDDDDB?9BDDDDDDDBBB?8,,######################################?12##################FFFFFCCC AS:i:0 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:1424:2423 69 X 16753128 0 * = 16753128 0 AGATNGGAAGAGCACACGTCTGAACTCCAGTCACCAAGGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACAAATACGGATGAGACATG CCCF#2ADHHHHHJJJJJJJJJJJJJJ>9:1*1C3C8D600)0*0*/00-.8B)--5B().).=).?CFFFBBBDB######################## AS:i:0 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:1424:2423 137 X 16753128 0 58S34M8S = 16753128 0 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAACAAAAAAAGAGATGAACAAGCAAA CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJHIHIIJJJJJJJHJJIIJJJHFFFFEEEEEEEDDDD################################## NM:i:0 AS:i:34 XS:i:29
HWI-1KL149:20:C1CU7ACXX:4:1101:2908:2463 97 12 110765491 60 70M30S = 110765491 70 AATTNGGGGAACAGCTTTCCAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATATTGGGCAAGATCGGAAGAGCACACGTCTGAACTCCAG CCCF#4BDHGHHHJJJJJJJJJIJHIJJJJJJJJJJJJJJJJIJJJJJJJJJJJJJIIIIHIJJJJIIIJIJJGHEHFFFEDDEEAA@BDDDCDDDD:C@ NM:i:1 AS:i:68 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:2908:2463 145 12 110765491 60 30S70M = 110765491 -70 CTCTTTCCCTACACGACGCTCTTCCGATCTAATTTGGGGAACAGCTTTCCAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATATTGGGCA DDDDDDDDDCAB=DDBDEEFFFFHHHJJJGHHGGFJJJJJIIIIJJJJJIJJJJJIJIIIJJJJJJJJJJJJIJJHHHFHEEJJIJJHHHHHFFFFFCBC NM:i:0 AS:i:70 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:4663:2297 81 4 114279632 60 100M = 114279455 -277 GATTCCTACTGCACCCATGGAGAATGTGCCTTTTACTGAAAGCAAATCCAAAATTCCTGTAAGGACTATGCCCACTTCCACCCCAGCACCTCCATNTGCA DCDDDDCACCDBCBCDDDCDDCCA?EEDDDFFDFFFHHHGHHHJJJJJJJJIJJIJIJJIJIJJJJJJJJJJIGJJIIHFIJJJJHGDHHDHDA2#FCCB NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:4663:2297 161 4 114279455 60 100M = 114279632 277 CGTGCAAACGGGTGATATACCTCCTCTCTCTGGTGTAAAGCAGATATCCTGCCCCGACTCTTCTGAACCAGCTGTACAAGTCCAGTTAGATTTTTCCACA CCBFFFFFHHHHFHIJJJJJIIJJJJJJJJJJJHIGIJIIJJJJJJJJJJHIJJJJJJJHHHHHHFDDDFDDEEEDDDADCCDDDCCDCCDEDDDCACCC NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:6872:2320 81 2 179597667 60 100M = 179597628 -139 GGCTGTGCCTTCCACAAATGCTATCCTGTATCTGTCAGAAGCAGCTATTTCTTTGCCATCCTTAAACCAGGACACCCTCATGGGGAGGGAGCCTGNAATT ABDDDDDBDDDDDDEDDEDDDEECEEFFFFFFHGHHHHJJIJJJJJIIJJIJJJJJJJJJIIJIHGJJJJJHHEJJIHJJJJJJJJJHHHHHDA2#FCCC NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:6872:2320 161 2 179597628 60 100M = 179597667 139 CCCTGCATCATTCATGTCTACTCTGATGATCTCCAAAGAGGCTGTGCCTTCCACAAATGCTATCCTGTATCTGTCAGAAGCAGCTATTTCTTTGCCATCC CCCFFFFFHHHHHJJJJJJJJJJJJIJJJJJJJJJJJJJJIIJJIIHJJJJIJJGIIIJJJIIJIIIHGIJJJJJIIEHHHHHHFBFFDEFECDECCDDA NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:9215:2408 97 2 220283746 60 100M = 220283863 217 CAGCNGCTCAAGGCCAAGTGAGGGCCCGGCACCCCAGACTCCTCTTTCTGCGGGCAGGGCACAGGAGGCTAGGCCTGGGGGCTGGGGTCCCGCTGTCAGC CCCF#2ADHHHHHFIJIIHIGIJJJJJJJJIIJJJJIJJJJJJJIIIJJIGFFFDDDDDDDBDDD?BDBDCBBDDCDDDDDBDDDBB>BBDDDDB@CDCD NM:i:2 AS:i:93 XS:i:23
HWI-1KL149:20:C1CU7ACXX:4:1101:9215:2408 145 2 220283863 60 100M = 220283746 -217 GCCCGGGACCCTCTCCTGCCCCATGTGGAGAAAGGGTCCTCCACCTGTGTGTTTCAAGGGGCCGTGACCTCCAGGTCTCTCCCCCTGCGATCCCATCTTG BDDBDBC?DDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDCADDDDDBEEEEEFFFFHHIJJJIHGJJJIJJJJJIIIIJIJJJJJHHHGHFFFFFCCC NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:9815:2325 97 22 46114322 60 100M = 46114410 188 AAAGNCCGGAATTGGTACAAGCCATGTTTCCCAAACTGAACAATCAAGAAAGGTAACCCCCCAACCAGCGTGGTCTGGAGTATTTAGCATTCCATATAGG CCCF#2ADHHHHHJJGHIJJJJJJJJIGJJJJJJJJJJJJJJJJJJJJGHIJJHIJJIIJJHFFFFDDCD?BDDDCCDCD>ACDEEDDDEDDEDCCCCCD NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:9815:2325 145 22 46114410 60 100M = 46114322 -188 ATTCCATATAGGGTATTCGATGCACGTGACTGAAAAGCTGTGTGGTTTCTGAGTTGGCACAGAATCTCTAAATACATGTTTCTGTGTTGGTAATGGTTTT DDCDEDCCDDDDCDDEEDEFFFFFHHHHIJJJJJJJIJJJJIIJJJIIGGJJJJJIJJJJJJJJIIHJJJJJIIJJJJJJJIIJIJIHFHHHFFFFFCCC NM:i:0 AS:i:100 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11401:2488 97 3 38763808 60 100M = 38763855 147 CCACNATACGGTAGCAAGTCTTGCGCACCTGCCAGCCCACATCCCATGGACTCTTCGTGGTATCCAGTTTGCAGCAGGGACAGTGGCGAATGCATCCTGT CCCF#4ADHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJEIJJIJJJHHHFFFFFFFEEEEEEEDABBDDDBBCCDBD>BDDDDEDDDD> NM:i:2 AS:i:93 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11401:2488 145 3 38763855 60 100M = 38763808 -147 GGACTCTTCGTGGTATCCAGTTTGCAGCAGGGACAGTGGCGAATGCATCCTGTGGGGAGAGGTGACTGATGGTGGGTGATGGCCAGTGGGCAAAGGGGAT DDCDDDB?DCCCDECDDCDDDCDDEEDEFFFFFFHHHJJIJJJIJIIJIJJJIJJIJJJJJJJJIJJJJJJJJJJIJJJJJJJJJJJHHHHHFFFFFCCC NM:i:1 AS:i:95 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11658:2375 97 7 35293037 60 100M = 35293129 192 CAGCNAGGGGCACAGACGGATGCGCAGCATCCCCAGTCCTCGGCGGACAGCCGGGTAGCCCAACTTACCCAGGGGTTTGATTGTGTTCTCCGTCGCCTCC CCCF#2ADHHHHHJIIJJJJIJJJJJJJJJIJJJJJIJJJJJJJJDDDDDDDDDDBBDDDDDDDDDDDDDDDDDDDBBBDDDDDDDDCEDCB?ABDBDD1 NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:11658:2375 145 7 35293129 60 100M = 35293037 -192 TCGCCTCCTTCTCCTTAGAGCCGCCGCTCGACATGAGCGCGGCAATGGAGAAGGCGTTGGCCCGGGAGGAGAGTTGGGGCTTGGGGGACGCCGTGAACTC DDBBBDDCA8DDDCC@DDDBDDDDDDDDDDEDDDDDDDDDDDDEDDDDCCDDDDFFFHHJJJJJJJJJHJJJJJJJJJJJJJJJJJJHHHHHFFFFDCBB NM:i:1 AS:i:95 XS:i:20
HWI-1KL149:20:C1CU7ACXX:4:1101:12054:2300 97 2 40401764 60 100M = 40401971 307 CAAGNTACATAAGATGTAGGTTTGGATTGATGGTTAAGGGTATTTGGGGAAAAATAAGGAACATTAAAAAAATAAGTCTTACCAAACAGGTATTTTCCTT CCCF#4=DHHHHHIJJHIJJHIJJJHIJJIIJJEGHJJJJDGIJJJJJJGHHIJJIIJJJIIIIJIJJHHFDEDECDDEEDDDDDDDDDDCCDEEEDDCD NM:i:1 AS:i:98 XS:i:0
HWI-1KL149:20:C1CU7ACXX:4:1101:12054:2300 145 2 40401971 60 100M = 40401764 -307 TTGTGAAGCCACCTAAAAAAGAAAAAAACAACAACAAATGTTATAATTTGACACTCTACATAACAAATACCAGTGACATCAGACTGCCTGACAACCCACC @CC@DDDDDDDDDDDDDDDDDDFHHHHEIIHIIIJJJIJJJJJJJJJIHDIJJJJJIIJJJJIJJJJHFJJJJJJIJJJJJJJJJJJHHHHHFFFFDBCB NM:i:0 AS:i:100 XS:i:0
Example (One FASTQ)
(compare to https://github.com/lh3/bwa/blob/master/example.c )
System.loadLibrary("bwajni");
BwaIndex index=new BwaIndex(new File("hg19.fa"));
BwaMem mem=new BwaMem(index);
KSeq kseq=new KSeq(new File("input.fastq.gz");
ShortRead read=null;
while((read=kseq.next())!=null)
{
for(AlnRgn a: mem.align(read))
{
if(a.getSecondary()>=0) continue;
System.out.println( read.getName()+"\t"+ a.getStrand()+"\t"+ a.getChrom()+"\t"+
a.getPos()+"\t"+ a.getMQual()+"\t"+ a.getCigar()+"\t"+ a.getNm() );
}
}
kseq.dispose();
index.close();
mem.dispose();
Testing
Here is the ouput of the JAVA version:
gunzip -c input.fastq.gz | head -n 4000 |\
java -Djava.library.path=src/main/native -cp src/main/java \
com.github.lindenb.jbwa.jni.Example human_g1k_v37.fasta -| tail
HWI-1KL149:20:C1CU7ACXX:4:1101:3077:33410 + 3 38647538 60 89M11S 1
HWI-1KL149:20:C1CU7ACXX:4:1101:3396:33445 + 8 52567289 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:10013:33288 - 1 156104115 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:10390:33496 - 6 123824853 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:13537:33483 + 2 157367092 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:14139:33390 + 20 31413797 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:14514:33458 + 2 179401813 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:15292:33282 + 15 63335820 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:16960:33276 - 12 110782784 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:17355:33322 + 6 126077895 60 100M 1
And the ouput of the Native C version:
gunzip -c input.fastq.gz | head -n 4000 |\
bwa-0.7.4/bwamem-lite human_g1k_v37.fasta - | tail
HWI-1KL149:20:C1CU7ACXX:4:1101:3077:33410 + 3 38647538 60 89M11S 1
HWI-1KL149:20:C1CU7ACXX:4:1101:3396:33445 + 8 52567289 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:10013:33288 - 1 156104115 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:10390:33496 - 6 123824853 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:13537:33483 + 2 157367092 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:14139:33390 + 20 31413797 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:14514:33458 + 2 179401813 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:15292:33282 + 15 63335820 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:16960:33276 - 12 110782784 60 100M 1
HWI-1KL149:20:C1CU7ACXX:4:1101:17355:33322 + 6 126077895 60 100M 1
GUI
As a test I also created a swing-Based interface for BWA:
java -Djava.library.path=src/main/native -cp src/main/java \
com.github.lindenb.jbwa.jni.BwaFrame human_g1k_v37.fasta
WEB-SERVICE
As an example I've implemented a WebService for BWA.
Server
The server is launched with make 'test.ws.server'
java -Djava.library.path=src/main/native -cp src/main/java com.github.lindenb.jbwa.ws.server.BWAServiceImpl \
-R human_g1k_v37.fasta -p 8081
Apr 26, 2013 9:54:34 PM com.github.lindenb.jbwa.ws.server.BWAServiceImpl main
INFO: Loading index for /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37.fasta
Apr 26, 2013 9:54:48 PM com.github.lindenb.jbwa.ws.server.BWAServiceImpl main
INFO: Service is published: http://localhost:8081/
once published, the server provides a WSDL -bases service description
<?xml version="1.0" encoding="UTF-8"?>
<!-- Published by JAX-WS RI at http://jax-ws.dev.java.net. RI's version is JAX-WS RI 2.2.4-b01. -->
<!-- Generated by JAX-WS RI at http://jax-ws.dev.java.net. RI's version is JAX-WS RI 2.2.4-b01. -->
<definitions xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:
wsp1_2="http://schemas.xmlsoap.org/ws/2004/09/policy" xmlns:wsam="http://www.w3.org/2007/05/addressing/metadata" xmlns:soap="http://schemas.xmlsoap.org/wsdl/
soap/" xmlns:tns="http://server.ws.jbwa.lindenb.github.com/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="http://schemas.xmlsoap.org/wsdl/" targetName
space="http://server.ws.jbwa.lindenb.github.com/" name="BWAServiceImplService">
<types>
<xsd:schema>
<xsd:import namespace="http://server.ws.jbwa.lindenb.github.com/" schemaLocation="http://localhost:8081/?xsd=1"/>
</xsd:schema>
</types>
<message name="align">
<part name="parameters" element="tns:align"/>
</message>
<message name="alignResponse">
<part name="parameters" element="tns:alignResponse"/>
</message>
<message name="Exception">
<part name="fault" element="tns:Exception"/>
</message>
<message name="getReferenceName">
<part name="parameters" element="tns:getReferenceName"/>
</message>
<message name="getReferenceNameResponse">
<part name="parameters" element="tns:getReferenceNameResponse"/>
</message>
<portType name="BWAService">
<operation name="align">
<input wsam:Action="http://server.ws.jbwa.lindenb.github.com/BWAService/alignRequest" message="tns:align"/>
<output wsam:Action="http://server.ws.jbwa.lindenb.github.com/BWAService/alignResponse" message="tns:alignResponse"/>
<fault message="tns:Exception" name="Exception" wsam:Action="http://server.ws.jbwa.lindenb.github.com/BWAService/align/Fault/Exception"/>
</operation>
<operation name="getReferenceName">
<input wsam:Action="http://server.ws.jbwa.lindenb.github.com/BWAService/getReferenceNameRequest" message="tns:getReferenceName"/>
<output wsam:Action="http://server.ws.jbwa.lindenb.github.com/BWAService/getReferenceNameResponse" message="tns:getReferenceNameResponse"/>
</operation>
</portType>
<binding name="BWAServiceImplPortBinding" type="tns:BWAService">
(...)
</binding>
<service name="BWAServiceImplService">
<port name="BWAServiceImplPort" binding="tns:BWAServiceImplPortBinding">
<soap:address location="http://localhost:8081/"/>
</port>
</service>
</definitions>
The Client
when the server is up and running, A client is generated for this service:
wsimport -keep -d tmp -p com.github.lindenb.jbwa.ws.client "http://localhost:8081/?wsdl"
The Makefile contains a target named 'test.ws.client' that reads a FASTQ, invoke the web-service and dump the result as XML:
gunzip -c test.fastq.gz |\
java -cp tmp com.github.lindenb.jbwa.ws.client.BWAServiceClient
Output:
<?xml version="1.0" encoding="UTF-8"?>
<bwa-service reference="human_g1k_v37.fasta">
<Alignment xmlns="" xmlns:ns2="http://server.ws.jbwa.lindenb.github.com/">
<chrom>1</chrom>
<cigar>13S87M</cigar>
<MQual>37</MQual>
<nm>1</nm>
<position>0</position>
<readBases>CCCCNCCCTGCTCACCGAGGCCCCCCTCAATCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTTGAGACCTTCAACGTGCCAGATCGGAAGAGC</readBases>
<readName>HWI-1KL149:20:C1CU7ACXX:4:1101:13638:2192 1:N:0:CAAGGAGC</readName>
<secondary>-1</secondary>
<strand>45</strand>
</Alignment>
<Alignment xmlns="" xmlns:ns2="http://server.ws.jbwa.lindenb.github.com/">
<chrom>2</chrom>
<cigar>82M18S</cigar>
<MQual>0</MQual>
<nm>5</nm>
<position>0</position>
<readBases>CCCCNCCCTGCTCACCGAGGCCCCCCTCAATCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTTGAGACCTTCAACGTGCCAGATCGGAAGAGC</readBases>
<readName>HWI-1KL149:20:C1CU7ACXX:4:1101:13638:2192 1:N:0:CAAGGAGC</readName>
<secondary>0</secondary>
<strand>43</strand>
</Alignment>
(...)