Nilesh Patra pushed to branch master at Debian Med / python-pyfaidx
Commits: f02905d7 by Nilesh Patra at 2020-12-12T18:30:04+05:30 routine-update: New upstream version - - - - - 008eb56e by Nilesh Patra at 2020-12-12T18:30:05+05:30 New upstream version 0.5.9.2 - - - - - 3faf6982 by Nilesh Patra at 2020-12-12T18:30:07+05:30 Update upstream source from tag 'upstream/0.5.9.2' Update to upstream version '0.5.9.2' with Debian dir ec2f0e7678798550c31510ad2cbeec3cbcf86944 - - - - - 29f8cad0 by Nilesh Patra at 2020-12-12T18:30:07+05:30 routine-update: Standards-Version: 4.5.1 - - - - - d7dc7eaf by Nilesh Patra at 2020-12-12T18:30:23+05:30 routine-update: Ready to upload to unstable - - - - - 3 changed files: - debian/changelog - debian/control - pyfaidx/__init__.py Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +python-pyfaidx (0.5.9.2-1) unstable; urgency=medium + + * Team upload. + * New upstream version + * Standards-Version: 4.5.1 (routine-update) + + -- Nilesh Patra <[email protected]> Sat, 12 Dec 2020 18:30:23 +0530 + python-pyfaidx (0.5.9.1-1) unstable; urgency=medium [ Andreas Tille ] ===================================== debian/control ===================================== @@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13), python3-mock, samtools, tabix <!nocheck> -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/python-pyfaidx Vcs-Git: https://salsa.debian.org/med-team/python-pyfaidx.git Homepage: https://github.com/mdshw5/pyfaidx ===================================== pyfaidx/__init__.py ===================================== @@ -29,7 +29,7 @@ if sys.version_info > (3, ): dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)') -__version__ = '0.5.9.1' +__version__ = '0.5.9.2' class KeyFunctionError(ValueError): @@ -659,11 +659,12 @@ class Faidx(object): # Calculate offset (https://github.com/samtools/htslib/blob/20238f354894775ed22156cdd077bc0d544fa933/faidx.c#L398) newlines_before = int( - (start0 - 1) / i.lenc * (i.lenb - i.lenc)) if start0 > 0 and i.lenc else 0 - newlines_to_end = int(end / i.lenc * (i.lenb - i.lenc)) if i.lenc else 0 + (start0 - 1) / i.lenc) if start0 > 0 and i.lenc else 0 + newlines_to_end = int(end / i.lenc) if i.lenc else 0 newlines_inside = newlines_to_end - newlines_before - seq_blen = newlines_inside + seq_len - bstart = i.offset + newlines_before + start0 + newline_blen = i.lenb - i.lenc + seq_blen = newlines_inside * newline_blen + seq_len + bstart = i.offset + newlines_before * newline_blen + start0 if seq_blen < 0 and self.strict_bounds: raise FetchError("Requested coordinates start={0:n} end={1:n} are " "invalid.\n".format(start, end)) @@ -674,7 +675,7 @@ class Faidx(object): with self.lock: if self._bgzf: # We can't add to virtual offsets, so we need to read from the beginning of the record and trim the beginning if needed self.file.seek(i.offset) - chunk = start0 + newlines_before + newlines_inside + seq_len + chunk = start0 + (newlines_before * newline_blen) + (newlines_inside * newline_blen) + seq_len chunk_seq = self.file.read(chunk).decode() seq = chunk_seq[start0 + newlines_before:] else: View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/0d6730165fd7ca690a02a150fb2767ac4bb00788...d7dc7eaf8b11cef65628aed56ac5659d290a7c6c -- View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/0d6730165fd7ca690a02a150fb2767ac4bb00788...d7dc7eaf8b11cef65628aed56ac5659d290a7c6c You're receiving this email because of your account on salsa.debian.org.
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