Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/samtools.py @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 import pysam.utils | |
| 2 | |
| 3 addreplacerg = pysam.utils.PysamDispatcher('samtools', 'addreplacerg') | |
| 4 ampliconclip = pysam.utils.PysamDispatcher('samtools', 'ampliconclip') | |
| 5 ampliconstats = pysam.utils.PysamDispatcher('samtools', 'ampliconstats') | |
| 6 bam2fq = pysam.utils.PysamDispatcher('samtools', 'bam2fq') | |
| 7 bamshuf = pysam.utils.PysamDispatcher('samtools', 'bamshuf') | |
| 8 bedcov = pysam.utils.PysamDispatcher('samtools', 'bedcov') | |
| 9 calmd = pysam.utils.PysamDispatcher('samtools', 'calmd') | |
| 10 cat = pysam.utils.PysamDispatcher('samtools', 'cat') | |
| 11 collate = pysam.utils.PysamDispatcher('samtools', 'collate') | |
| 12 consensus = pysam.utils.PysamDispatcher('samtools', 'consensus') | |
| 13 coverage = pysam.utils.PysamDispatcher('samtools', 'coverage') | |
| 14 cram_size = pysam.utils.PysamDispatcher('samtools', 'cram-size') | |
| 15 depad = pysam.utils.PysamDispatcher('samtools', 'depad') | |
| 16 depth = pysam.utils.PysamDispatcher('samtools', 'depth') | |
| 17 dict = pysam.utils.PysamDispatcher('samtools', 'dict') | |
| 18 faidx = pysam.utils.PysamDispatcher('samtools', 'faidx') | |
| 19 fasta = pysam.utils.PysamDispatcher('samtools', 'fasta') | |
| 20 fastq = pysam.utils.PysamDispatcher('samtools', 'fastq') | |
| 21 fixmate = pysam.utils.PysamDispatcher('samtools', 'fixmate') | |
| 22 flags = pysam.utils.PysamDispatcher('samtools', 'flags') | |
| 23 flagstat = pysam.utils.PysamDispatcher('samtools', 'flagstat') | |
| 24 fqidx = pysam.utils.PysamDispatcher('samtools', 'fqidx') | |
| 25 fqimport = pysam.utils.PysamDispatcher('samtools', 'import') | |
| 26 head = pysam.utils.PysamDispatcher('samtools', 'head') | |
| 27 idxstats = pysam.utils.PysamDispatcher('samtools', 'idxstats') | |
| 28 index = pysam.utils.PysamDispatcher('samtools', 'index') | |
| 29 markdup = pysam.utils.PysamDispatcher('samtools', 'markdup') | |
| 30 merge = pysam.utils.PysamDispatcher('samtools', 'merge') | |
| 31 mpileup = pysam.utils.PysamDispatcher('samtools', 'mpileup') | |
| 32 pad2unpad = pysam.utils.PysamDispatcher('samtools', 'pad2unpad') | |
| 33 phase = pysam.utils.PysamDispatcher('samtools', 'phase') | |
| 34 quickcheck = pysam.utils.PysamDispatcher('samtools', 'quickcheck') | |
| 35 reference = pysam.utils.PysamDispatcher('samtools', 'reference') | |
| 36 reheader = pysam.utils.PysamDispatcher('samtools', 'reheader') | |
| 37 reset = pysam.utils.PysamDispatcher('samtools', 'reset') | |
| 38 rmdup = pysam.utils.PysamDispatcher('samtools', 'rmdup') | |
| 39 samples = pysam.utils.PysamDispatcher('samtools', 'samples') | |
| 40 sort = pysam.utils.PysamDispatcher('samtools', 'sort') | |
| 41 split = pysam.utils.PysamDispatcher('samtools', 'split') | |
| 42 stats = pysam.utils.PysamDispatcher('samtools', 'stats') | |
| 43 targetcut = pysam.utils.PysamDispatcher('samtools', 'targetcut') | |
| 44 tview = pysam.utils.PysamDispatcher('samtools', 'tview') | |
| 45 version = pysam.utils.PysamDispatcher('samtools', 'version') | |
| 46 view = pysam.utils.PysamDispatcher('samtools', 'view') | |
| 47 | |
| 48 __all__ = [ | |
| 49 'addreplacerg', 'ampliconclip', 'ampliconstats', | |
| 50 'bam2fq', 'bamshuf', 'bedcov', 'calmd', 'cat', | |
| 51 'collate', 'consensus', 'coverage', 'cram_size', | |
| 52 'depad', 'depth', 'dict', 'faidx', 'fasta', | |
| 53 'fastq', 'fixmate', 'flags', 'flagstat', 'fqidx', | |
| 54 'fqimport', 'head', 'idxstats', 'index', | |
| 55 'markdup', 'merge', 'mpileup', 'pad2unpad', | |
| 56 'phase', 'quickcheck', 'reference', 'reheader', | |
| 57 'reset', 'rmdup', 'samples', 'sort', 'split', | |
| 58 'stats', 'targetcut', 'tview', 'version', 'view', | |
| 59 ] |