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Sam2Tsv
Pierre Lindenbaum edited this page May 30, 2016
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##Motivation
Prints the SAM alignments as a TAB delimited file.
##Compilation
Since 2016-05-30 the compilation of the "Java API for high-throughput sequencing data (HTS) formats" (htsjdk) library requires gradle http://gradle.org
- java compiler SDK 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 ) - GNU Make > 3.81
- curl/wget
- git
- gradle http://gradle.org is only required to compile the "Java API for high-throughput sequencing data (HTS) formats" (htsjdk)
- xsltproc http://xmlsoft.org/XSLT/xsltproc2.html
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make sam2tsvby default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by addinging standalone=yes on the command line:
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make sam2tsv standalone=yesThe required libraries will be downloaded and installed in the dist directory.
The a file local.mk can be created edited to override/add some definitions.
For example it can be used to set the HTTP proxy:
http.proxy.host=your.host.com
http.proxy.port=124567
to set the gradle user home ( https://docs.gradle.org/current/userguide/build_environment.html#sec:gradle_properties_and_system_properties )
gradle.user.home=/dir1/dir2/gradle_user_home
##Synopsis
$ java -jar dist/sam2tsv.jar [options] (stdin|file.bam|file.sam) - -o|--output (OUTPUT-FILE) Output file. Default:stdout.
- -r|--REF (FASTA) indexed Fasta sequence
- -A|--printAlignments Print Alignments Default value : "false".
- -h|--help print help
- -version|--version show version and exit
##Source Code
Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv.java
Columns are:
- read name
- read flags
- reference name
- read-pos
- read-base
- read-qual
- ref-pos
- ref-base
- cigar-op
$ java -jar dist/sam2tsv.jar -A \
-r samtools-0.1.18/examples/toy.fa
samtools-0.1.18/examples/toy.sam
r001 163 ref 0 T . 7 T M
r001 163 ref 1 T . 8 T M
r001 163 ref 2 A . 9 A M
r001 163 ref 3 G . 10 G M
r001 163 ref 4 A . 11 A M
r001 163 ref 5 T . 12 T M
r001 163 ref 6 A . 13 A M
r001 163 ref 7 A . 14 A M
r001 163 ref 8 A . . . I
r001 163 ref 9 G . . . I
r001 163 ref 10 A . . . I
r001 163 ref 11 G . . . I
r001 163 ref 12 G . 15 G M
r001 163 ref 13 A . 16 A M
r001 163 ref 14 T . 17 T M
r001 163 ref 15 A . 18 A M
r001 163 ref . . . 19 G D
r001 163 ref 16 C . 20 C M
r001 163 ref 17 T . 21 T M
r001 163 ref 18 G . 22 G M
: ref 7 TTAGATAAAGAGGATA-CTG 22
: |||||||| |||| |||
: r001 1 TTAGATAA----GATAGCTG 19
r002 0 ref 1 A . . . I
r002 0 ref 2 A . . . I
r002 0 ref 3 A . 9 A M
r002 0 ref 4 G . 10 G M
r002 0 ref 5 A . 11 A M
r002 0 ref 6 T . 12 T M
r002 0 ref 7 A . 13 A M
r002 0 ref 8 A . 14 A M
r002 0 ref 9 G . . . I
r002 0 ref 10 G . . . I
r002 0 ref 11 G . 15 G M
r002 0 ref 12 A . 16 A M
r002 0 ref 13 T . 17 T M
r002 0 ref 14 A . 18 A M
r002 0 ref 15 A . . . I
r002 0 ref 16 A . . . I
: ref 8 AAAGATAAGGGATAAA 18
: |||||| ||||
: r002 1 --AGATAA--GATA-- 17
r003 0 ref 0 A . 9 A M
r003 0 ref 1 G . 10 G M
r003 0 ref 2 C . 11 A M
r003 0 ref 3 T . 12 T M
r003 0 ref 4 A . 13 A M
r003 0 ref 5 A . 14 A M
: ref 4 AGCTAA 14
: || |||
: r003 1 AGATAA 6
r004 0 ref 0 A . 16 A M
r004 0 ref 1 T . 17 T M
r004 0 ref 2 A . 18 A M
r004 0 ref 3 G . 19 G M
r004 0 ref 4 C . 20 C M
r004 0 ref 5 T . 21 T M
r004 0 ref . . . 22 G N
r004 0 ref . . . 23 T N
r004 0 ref . . . 24 G N
r004 0 ref . . . 25 C N
r004 0 ref . . . 26 T N
r004 0 ref . . . 27 A N
r004 0 ref . . . 28 G N
r004 0 ref . . . 29 T N
r004 0 ref . . . 30 A N
r004 0 ref . . . 31 G N
r004 0 ref . . . 32 G N
r004 0 ref . . . 33 C N
r004 0 ref . . . 34 A N
r004 0 ref . . . 35 G N
r004 0 ref 6 C . . . I
r004 0 ref 7 T . 36 T M
r004 0 ref 8 C . 37 C M
r004 0 ref 9 A . 38 A M
r004 0 ref 10 G . 39 G M
r004 0 ref 11 C . 40 C M
: ref 16 ATAGCT--------------CTCAGC 40
: |||||| |||||
: r004 1 ATAGCTGTGCTAGTAGGCAG-TCAGC 12
r003 16 ref 0 T . 29 T M
r003 16 ref 1 A . 30 A M
r003 16 ref 2 G . 31 G M
r003 16 ref 3 G . 32 G M
r003 16 ref 4 C . 33 C M
: ref 23 TAGGC 33
: |||||
: r003 1 TAGGC 5
r001 83 ref 0 C . 37 C M
r001 83 ref 1 A . 38 A M
r001 83 ref 2 G . 39 G M
r001 83 ref 3 C . 40 C M
r001 83 ref 4 G . 41 G M
r001 83 ref 5 C . 42 C M
r001 83 ref 6 C . 43 C M
r001 83 ref 7 A . 44 A M
r001 83 ref 8 T . 45 T M
: ref 37 CAGCGCCAT 45
: |||||||||
: r001 1 CAGCGCCAT 9
x1 0 ref2 0 A 30 1 a M
x1 0 ref2 1 G 30 2 g M
x1 0 ref2 2 G 30 3 g M
x1 0 ref2 3 T 30 4 t M
x1 0 ref2 4 T 30 5 t M
x1 0 ref2 5 T 30 6 t M
x1 0 ref2 6 T 30 7 t M
x1 0 ref2 7 A 30 8 a M
x1 0 ref2 8 T 30 9 t M
x1 0 ref2 9 A 30 10 a M
x1 0 ref2 10 A 30 11 a M
x1 0 ref2 11 A 30 12 a M
x1 0 ref2 12 A 30 13 a M
x1 0 ref2 13 C 30 14 c M
x1 0 ref2 14 A 30 15 a M
x1 0 ref2 15 A 30 16 a M
x1 0 ref2 16 A 30 17 t M
x1 0 ref2 17 T 30 18 t M
x1 0 ref2 18 A 30 19 a M
x1 0 ref2 19 A 30 20 a M
: ref2 1 AGGTTTTATAAAACAAATAA 20
: |||||||||||||||| |||
: x1 1 aggttttataaaacaattaa 20
x2 0 ref2 0 G 30 2 g M
x2 0 ref2 1 G 30 3 g M
x2 0 ref2 2 T 30 4 t M
x2 0 ref2 3 T 30 5 t M
x2 0 ref2 4 T 30 6 t M
x2 0 ref2 5 T 30 7 t M
x2 0 ref2 6 A 30 8 a M
x2 0 ref2 7 T 30 9 t M
x2 0 ref2 8 A 30 10 a M
x2 0 ref2 9 A 30 11 a M
x2 0 ref2 10 A 30 12 a M
x2 0 ref2 11 A 30 13 a M
x2 0 ref2 12 C 30 14 c M
x2 0 ref2 13 A 30 15 a M
x2 0 ref2 14 A 30 16 a M
x2 0 ref2 15 A 30 17 t M
x2 0 ref2 16 T 30 18 t M
x2 0 ref2 17 A 30 19 a M
x2 0 ref2 18 A 30 20 a M
x2 0 ref2 19 T 30 21 g M
x2 0 ref2 20 T 30 22 t M
: ref2 2 GGTTTTATAAAACAAATAATT 22
: ||||||||||||||| ||| |
: x2 1 ggttttataaaacaattaagt 21
(...)
- Moved to a standard argc/argv command line
- 2014-04: added qual and samflag. Fixed a bug in soft-clip
- 2014-11: manage hard+soft clip
Sam2tsv was cited in :
- Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements* . McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, et al. (2014) Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements. PLoS ONE 9(9): e106689. doi: 10.1371/journal.pone.0106689 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106689
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
The project is licensed under the MIT license.
Should you cite sam2tsv ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030