Describe the bug
the qpileup merge mode run failed, it throws the error message "different reference files ". The reason is the merge mode check H5 header, and checks the reference file if the header line contains the substring "bootstrap". In this run, an H5 file path contains a "bootstrap" string, it is not a reference file for bootstrap mode; however, this pileup run treats it as a reference file.
To Reproduce
Steps to reproduce the behavior:
INI file "add" mode, add H5 files with a path containing "bootstrap" substring.
pass this INI file to qpileup
add the above output (H5) to the INI file "merge" mode.
pass this INI file to qpileup
Expected behavior
allow file path contains any operation system allowed string
Screenshots
13:51:18.264 [main] INFO org.qcmg.pileup.mode.MergeMT - HDF file to merge from: /mnt/lustre/working/genomeinfo/share/qpileup/20210830/add/splitAdd/bootstrap_default/exonA.h5
13:51:18.266 [main] INFO org.qcmg.pileup.mode.MergeMT - HDF file to merge from: /mnt/lustre/working/genomeinfo/share/qpileup/20210830/add/splitAdd/bootstrap_default/exonB.h5
13:51:18.267 [main] INFO org.qcmg.pileup.mode.MergeMT - HDF file to merge from: /mnt/lustre/working/genomeinfo/share/qpileup/20210830/add/splitAdd/bootstrap_default/exonC.h5
13:51:18.284 [main] SEVERE org.qcmg.pileup.mode.MergeMT - Setting exit status to 1 as error caught in execute thread: org.qcmg.pileup.QPileupException: HDF files cannot be merged as they have different reference files - file one: /mnt/lustre/reference/genomes/GRCh37_ICGC_standard_v2/primary_files/GRCh37_ICGC_standard_v2.fa | file2 : lustre/working/genomeinfo/sample/7/6/76a8c12a-48e0-47b6-85ba-ea39577f3a35/aligned_read_group_set/44aeedb0-9e4c-4487-9420-2b75f62eeacd.bam
at org.qcmg.pileup.hdf.MetadataRecordDS.checkHDFMetadata(MetadataRecordDS.java:215)
at org.qcmg.pileup.mode.MergeMT.setupMetadata(MergeMT.java:181)
at org.qcmg.pileup.mode.MergeMT.execute(MergeMT.java:95)
at org.qcmg.pileup.PileupPipeline.runPipeline(PileupPipeline.java:48)
at org.qcmg.pileup.QPileup.runPileup(QPileup.java:69)
at org.qcmg.pileup.QPileup.main(QPileup.java:25)
Desktop (please complete the following information):
Describe the bug the qpileup merge mode run failed, it throws the error message "different reference files ". The reason is the merge mode check H5 header, and checks the reference file if the header line contains the substring "bootstrap". In this run, an H5 file path contains a "bootstrap" string, it is not a reference file for bootstrap mode; however, this pileup run treats it as a reference file.
To Reproduce Steps to reproduce the behavior:
Expected behavior allow file path contains any operation system allowed string
Screenshots
Desktop (please complete the following information):
Additional context Nil