The location of FileMerge is determined through a symbolic link in the PATH environment. Some wrapper scripts are thus required to call FileMerge from Subversion.īash scripts for this task can be checked-out from this repository or downloaded as an archive.įour scripts are provided: fmdiff, fmdiff3, fmresolve and fmmerge. it forks and does not block) and it expects different arguments. It can be opened from the command line with the opendiff command, but its interface differs from that of diff and diff3. Worthless to find interline changes in long linesĪpple's Developer Tools for Mac OS X include FileMerge, a graphical tool to compare and merge files.įileMerge can be much handier to use unfortunately, it doesn't integrate with Subversion straightforwardly.They do have some limitations though, including: The built-in diff and diff3 tools (from diffutils) go a long way to provide this functionality for text files on the command line. Subversion principally uses the copy-modify-merge versioning model to allow concurrent collaboration on the same set of files.įor this to work well, it is crucial to have good tools to view and merge the differences between files. The official website (and official version) can be found at: These scripts were created by Bruno De Fraine. doi:10.1002/cncy.Using FileMerge as a diff command for Subversion Multiplatform comparison of molecular oncology tests performed on cytology specimens and formalin-fixed, paraffin-embedded tissue. Adequacy of samples obtained by EBUS TBNA for molecular analysis in patients with non-small cell lung cancer. Labarca G, Folch E, Jantz M, Mehta HJ, Majid A, Fernandez-Bussy S. Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group. Molecular testing guideline for the selection of lung cancer patients for treatment with targeted tyrosine kinase inhibitors: American Society of Clinical Oncology endorsement summary of the College of American Pathologists/International Association for the Study of Lung Cancer/Association for Molecular Pathology clinical practice guideline update. Endobronchial ultrasound-guided transbronchial needle aspiration cytology: a state of the art review. Cancer Cytopathology published by Wiley Periodicals LLC on behalf of American Cancer Society.Ĭameron SEH, Andrade RS, Pambuccian SE. TruSight Oncology 500 (TSO500) cytology endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) lung cancer molecular diagnostics. Microscopy of Diff-Quik smears can triage samples for comprehensive panel sequencing, which highlights smears as an excellent alternative to traditional testing with cell blocks. Smears were scored for tumor mutation burden. Tier 1/2 mutations were discovered in two cases where standard-of-care specimens were inadequate for sequencing. All standard-of-care mutations were detected in replicate smears from individual patients, regardless of malignant cell content. Low-malignant-cell content (<25%) and smear area (<15%) were the main reasons for failure. Fifty DNA samples (89%) with varying malignant yields were successfully sequenced. An algorithm was developed that predicted a >50-ng DNA yield of a smear with an area under the curve of 0.86. DNA from 56 smears from 27 patients was sequenced with the TruSight Oncology 500 assay (Illumina).Įach microscopy parameter had a significant effect on the DNA yield. One hundred eighty-five smears were evaluated by microscopy to estimate malignant cell percentage and abundance and to calculate smear size and were subjected to DNA extraction. All patients had air-dried, Diff-Quik cytology smears and formalin-fixed, paraffin-embedded cell blocks collected for cytopathology and molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels.Ī prospective study was performed on samples from 66 patients with malignant lymph nodes who underwent EBUS TBNA. Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing.
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