hello,
I would like to convert my sam file (.sam) to another type is .axt format.
i used BWA for alignement but the output of this tool is .sam format.
Can you help me?
Thanks
I quickly wrote a converter https://github.com/lindenb/jvarkit/wiki/Biostar170742
$ java -jar dist-2.0.1/biostar170742.jar \
-R ref.fa \
S1.bam
0 rotavirus 1 70 rotavirus_1_317_5:0:0_7:0:0_2de/1 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAATATGGCGTCAACTCAGCAGATGGTCAGCTCTAATATT
1 rotavirus 1 70 rotavirus_1_535_4:0:0_4:0:0_1a6/2 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTACTGCTTTTCAGTGGTTGCTTCTCAAGATGGAGTGTACTCATCAGATGGTAAGCTCTATTATT
2 rotavirus 1 70 rotavirus_1_543_5:0:0_11:0:0_390/2 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTAATGCTTTTCATTTGATGCTGCTCAAGATGGAGTCTACACAGCAGATGGTCAGCTCTATTATT
3 rotavirus 1 70 rotavirus_1_578_3:0:0_7:0:0_7c/1 + 60
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT
GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTCCTGAGCAGCTGGTAAGCTCTATTATT
(...)
I installed the tool. but I can't run Biostar70742.java
there are errors.
[m@rainman biostar]$ javac Biostar170742.java
you didn't follow the instructions: https://github.com/lindenb/jvarkit/wiki/Biostar170742
make biostar170742
same problem BUILD Failed.
[mk@rainman jvarkit]$ make biostar170742
echo "Compiling htsjdk with ${JAVA_HOME} = "
Compiling htsjdk with =
echo "Compiling htsjdk library for java. Requires apache ANT. If it fails here, it's a not a problem with jvarkit."
Compiling htsjdk library for java. Requires apache ANT. If it fails here, it's a not a problem with jvarkit.
echo "And ${JAVA_HOME}/bin/javac should be >=1.8"
And /bin/javac should be >=1.8
(cd /home/mk/jvarkit/htsjdk-2.0.1 && ant )
Buildfile: build.xml
write-version-property:
BUILD FAILED
/home/mk/jvarkit/htsjdk-2.0.1/build.xml:64: Problem: failed to create task or type propertyfile
Cause: the class org.apache.tools.ant.taskdefs.optional.PropertyFile was not found.
This looks like one of Ant's optional components.
Action: Check that the appropriate optional JAR exists in
-/usr/share/ant/lib
-/home/mk/.ant/lib
-a directory added on the command line with the -lib argument
Do not panic, this is a common problem.
The commonest cause is a missing JAR.
This is not a bug; it is a configuration problem
Total time: 0 seconds
make: *** [/home/mk/jvarkit/htsjdk-2.0.1/dist/htsjdk-2.0.1.jar] Erreur 1
[mk@rainman jvarkit]$
as it is described "ant-optional" is missing...
try googling please.
forgot to put the read positions: udpated the source https://github.com/lindenb/jvarkit/commit/84dfac8015be3ae66cdb15b25618022198b8f106
does AXT supports INDELS (like SAM)?
yes. it support indels
so, how does it look likes with indels, I cannot find an example
this is an example:
so how convert
.samoutput to.axt?i cant install ant in my server!!! have you solution?
you don't need to be root to install ant, just download and put it anywhere: https://ant.apache.org/bindownload.cgi
I installed apache.
but no run to biostar170742.
https://ant.apache.org/manual/install.html#optionalTasks
thank you but I cant install apache. I don't know the problem
have you another solution to run samtoaxt.java?
Thanks