public static Platform getPlatform(MaPSeqDAOBean mapseqDAOBean, JSONObject jsonObject) throws JSONException { logger.info("ENTERING getPlatform(MaPSeqDAOBean, JSONObject)"); Platform platform = null; if (jsonObject.has("guid")) { Long guid = jsonObject.getLong("guid"); try { platform = mapseqDAOBean.getPlatformDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); } } if (platform == null) { logger.warn("No Platform found"); return null; } logger.debug("Found Platform: {}", platform.toString()); return platform; }
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPID, String.format("%s-%s_L%03d", sequencerRun.getName(), htsfSample.getBarcode(), htsfSample.getLaneIndex())); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, htsfSample.getBarcode()); job.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY,
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
public static Platform getPlatform(MaPSeqDAOBean mapseqDAOBean, JSONObject jsonObject) throws JSONException { logger.info("ENTERING getPlatform(MaPSeqDAOBean, JSONObject)"); Platform platform = null; if (jsonObject.has("guid")) { Long guid = jsonObject.getLong("guid"); try { platform = mapseqDAOBean.getPlatformDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); } } if (platform == null) { logger.warn("No Platform found"); return null; } logger.debug("Found Platform: {}", platform.toString()); return platform; }
htsfSample.getName()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, htsfSample.getName());
sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument( PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform() .getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument( PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, sampleName);
picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun .getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob .addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, sampleName);
picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPLIBRARY, sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun .getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob .addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, sampleName);
sampleName); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORM, sequencerRun.getPlatform().getInstrument()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPPLATFORMUNIT, sequencerRun.getPlatform().getInstrumentModel()); picardAddOrReplaceReadGroupsJob.addArgument(PicardAddOrReplaceReadGroupsCLI.READGROUPSAMPLENAME, sampleName);