From cba5635d61cf9ae9e10f81a367d08b48baa0c865 Mon Sep 17 00:00:00 2001 From: jscaber Date: Wed, 24 Nov 2021 12:01:36 +0000 Subject: [PATCH 1/3] fix other instance of pysam --- cgat/BamTools/geneprofile.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cgat/BamTools/geneprofile.pyx b/cgat/BamTools/geneprofile.pyx index bfc75b2c..c29f482e 100644 --- a/cgat/BamTools/geneprofile.pyx +++ b/cgat/BamTools/geneprofile.pyx @@ -1,7 +1,7 @@ #cimport csamtools from pysam.libchtslib cimport * -from pysam.libcalignmentfile cimport * +from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment import pysam import collections, array, struct, sys, itertools From 2a75a44676548fe777be5632174ec2048801cb54 Mon Sep 17 00:00:00 2001 From: jscaber Date: Wed, 24 Nov 2021 12:19:12 +0000 Subject: [PATCH 2/3] fix other instance --- cgat/BamTools/peakshape.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cgat/BamTools/peakshape.pyx b/cgat/BamTools/peakshape.pyx index 508a317e..8cd014fc 100644 --- a/cgat/BamTools/peakshape.pyx +++ b/cgat/BamTools/peakshape.pyx @@ -1,6 +1,6 @@ #cimport csamtools -from pysam.libcalignmentfile cimport * +from pysam.libcalignmentfile cimport AlignmentFile, AlignedSegment import collections import cgatcore.experiment as E import numpy From cc011c5a159225fa4f83504c4e4efd095c443e0a Mon Sep 17 00:00:00 2001 From: jscaber Date: Wed, 24 Nov 2021 12:24:44 +0000 Subject: [PATCH 3/3] final instance of libcalaligmen --- cgat/GeneModelAnalysis.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cgat/GeneModelAnalysis.pyx b/cgat/GeneModelAnalysis.pyx index e0463d36..5633d4cf 100644 --- a/cgat/GeneModelAnalysis.pyx +++ b/cgat/GeneModelAnalysis.pyx @@ -1,7 +1,7 @@ # cython: profile=True #cimport csamtools from pysam.libchtslib cimport * -from pysam.libcalignmentfile cimport * +from pysam.libcalignmentfile cimport AlignedSegment from posix.stdlib cimport drand48 import collections, array, struct