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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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BamStats04 does not recognize IN= or I= #24

Closed apelin20 closed 9 years ago

apelin20 commented 9 years ago

Hello, This is a bit odd:

@BioPower3-IBM ~/Rozella/mapping $ ll total 17G drwxrwxr-x. 2 adrian adrian 4.0K Mar 26 15:15 . drwxrwxr-x. 6 adrian adrian 4.0K Mar 26 12:33 .. -rw-rw-r--. 1 adrian adrian 0 Mar 26 15:18 Contig_coverage.table -rw-rw-r--. 1 adrian adrian 23K Mar 26 14:39 Contig_ranges2.bed -rw-rw-r--. 1 adrian adrian 25K Mar 26 14:34 Contigs.stats -rw-rw-r--. 1 adrian adrian 6.5G Mar 26 13:39 Rozella.bam -rw-rw-r--. 1 adrian adrian 5.1G Mar 26 14:16 Rozella.sort.bam -rw-rw-r--. 1 adrian adrian 5.1G Mar 26 14:57 Rozella.sort.grp.bam -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 15:22:35 @BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 IN=Rozella.sort.grp.bam BED=Contig_ranges2.bed VALIDATION_STRINGENCY=LENIENT > Contig_coverage.table ERROR: Option 'IN' is required. ... @BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 IN=Rozella.sort.grp.bam BED=Contig_ranges2.bed ERROR: Option 'IN' is required. ... @BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 IN="Rozella.sort.grp.bam" BED=Contig_ranges2.bed VALIDATION_STRINGENCY=LENIENT > Contig_coverage.table ERROR: Option 'IN' is required. ... @BioPower3-IBM ~/Rozella/mapping $ ~/programs/jvarkit/dist-1.128/bamstats04 I=Rozella.sort.grp.bam BED=Contig_ranges2.bed VALIDATION_STRINGENCY=LENIENT > Contig_coverage.table ERROR: Option 'IN' is required. ...

Any idea what could be going on? I tried other BAM files too, same issue. Adrian

lindenb commented 9 years ago

yes there was a bug in my Makefile creating the bash wrapper, I fixed it a few days ago: https://github.com/lindenb/jvarkit/commit/fe6480ef56d91e683467200bbe805a726c4c6457

you could also just use the jar command:

java -jar ~/programs/jvarkit/dist-1.128/bamstats04.jar I=Rozella.sort.grp.bam BED=Contig_ranges2.bed VALIDATION_STRINGENCY=LENIENT

tell me if that works.

apelin20 commented 9 years ago

It does indeed! I also recompiled and the binary also works now. Thanks!