Commit 5aa6792b authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.14+ds

parent f3bd90ac

.gitignore

+2 −0
Original line number Diff line number Diff line
@@ -14,6 +14,7 @@ tests/*.sam 
tests/*.fai

tests/pysam_data

tests/cbcf_data

tests/tabix_data



samtools/config.h

htslib/config.status
@@ -52,6 +53,7 @@ var/ 
*.egg-info/

.installed.cfg

*.egg

doc/_build



# Installer logs

pip-log.txt

MANIFEST.in

+6 −34
Original line number Diff line number Diff line
@@ -17,16 +17,22 @@ include pysam/libc*.c 
include pysam/*.c

include pysam/*.h



# exclude tests from pypi tar-ball - they

# require additional data

prune tests/



# samtools

include samtools/configure

include samtools/config.mk.in

include samtools/config.h.in

include samtools/*.h

include samtools/*.c

exclude samtools/config.h

include samtools/*/*.h



# bcftools

include bcftools/*.h

include bcftools/*.c

exclude bcftools/config.h



# htslib
@@ -50,39 +56,5 @@ include cy_build.py 
include pysam.py

include requirements.txt



# pysam tests

include tests/00README.txt

include tests/pysam_data

include tests/tabix_data

include tests/*.py

#ex1.fa

#include tests/ex1.sam.gz

#include tests/ex3.sam

#include tests/ex4.sam

#include tests/ex5.sam

#include tests/ex6.sam

#include tests/ex7.sam

#include tests/ex8.sam

#include tests/ex9_fail.bam

#include tests/ex9_nofail.bam

#include tests/ex10.sam

#include tests/example.py

#include tests/pysam_test.py

#include tests/segfault_tests.py

#include tests/example_*.sam

#include tests/example_btag.bam

#include tests/tag_bug.bam

#include tests/example.vcf40

#include tests/example_empty_header.bam

#include tests/test_unaligned.bam

#include tests/issue100.bam



# tabix tests

#include tests/example.gtf.gz

#include tests/example.gtf.gz.tbi

#include tests/example.bed.gz

#include tests/example.bed.gz.tbi

#include tests/vcf-examples/*.vcf



# documentation

include doc/*

NEWS

+49 −1
Original line number Diff line number Diff line
@@ -5,6 +5,55 @@ http://pysam.readthedocs.io/en/latest/release.html 
Release notes

=============



Release 0.14.0

==============



This release wraps htslib/samtools versions 1.7.0.



* SAM/BAM/CRAM headers are now managed by a separate AlignmentHeader

  class.

* AlignmentFile.header.as_dict() returns an ordered dictionary.

* Use "stop" instead of "end" to ensure consistency to

  VariantFile. The end designations have been kept for backwards

  compatibility.



* [#611] and [#293] CRAM repeated fetch now works, each iterator

  reloads index if multiple_iterators=True

* [#608] pysam now wraps htslib 1.7 and samtools 1.7.

* [#580] reference_name and next_reference_name can now be set to "*"

  (will be converted to None to indicate an unmapped location)

* [#302] providing no coordinate to count_coverage will not count from

  start/end of contig.

* [#325] @SQ records will be automatically added to header if they are

  absent from text section of header.

* [#529] add get_forward_sequence() and get_forward_qualities()

  methods

* [#577] add from_string() and to_dict()/from_dict() methods to

  AlignedSegment. Rename tostring() to to_string() throughout for

  consistency

* [#589] return None from build_alignment_sequence if no MD tag is set

* [#528] add PileupColumn.__len__ method



Backwards incompatible changes:



* AlignmentFile.header now returns an AlignmentHeader object. Use

  AlignmentFile.header.to_dict() to get the dictionary as

  previously. Most dictionary accessor methods (keys(), values(),

  __getitem__, ...) have been implemented to ensure some level of

  backwards compatibility when only reading.



  The rationale for this change is to have consistency between

  AlignmentFile and VariantFile.

  	      

* AlignmentFile and FastaFile now raise IOError instead of OSError



Medium term we plan to have a 1.0 release. The pysam

interface has grown over the years and the API is cluttered with

deprecated names (Samfile, getrname(), gettid(), ...). To work towards

this, the next release (0.15.0) will yield DeprecationWarnings 

for any parts of the API that are considered obsolete and will not be

in 1.0. Once 1.0 has been reached, we will use semantic versioning.



Release 0.13.0

===============
@@ -20,7 +69,6 @@ contains a series of bugfixes. 
* [#537] allow tabix index files to be created in a custom location.

* [#530] add get_index_statistics() method





Release 0.12.0.1

================

bcftools/HMM.c.pysam.c

+1 −1
Original line number Diff line number Diff line 
#include "pysam.h"

#include "bcftools.pysam.h"



/* The MIT License

bcftools/bam2bcf.c.pysam.c

+5 −5
Original line number Diff line number Diff line 
#include "pysam.h"

#include "bcftools.pysam.h"



/*  bam2bcf.c -- variant calling.
@@ -108,7 +108,7 @@ static int get_position(const bam_pileup1_t *p, int *len) 
        if ( cig==BAM_CHARD_CLIP ) continue;

        if ( cig==BAM_CPAD ) continue;

        if ( cig==BAM_CREF_SKIP ) continue;

        fprintf(pysam_stderr,"todo: cigar %d\n", cig);

        fprintf(bcftools_stderr,"todo: cigar %d\n", cig);

        assert(0);

    }

    *len = n_tot_bases;
@@ -504,7 +504,7 @@ void calc_SegBias(const bcf_callret1_t *bcr, bcf_call_t *call) 
    double sum = 0;

    const double log2 = log(2.0);



    // fprintf(pysam_stderr,"M=%.1f  p=%e q=%e f=%f  dp=%d\n",M,p,q,f,avg_dp);

    // fprintf(bcftools_stderr,"M=%.1f  p=%e q=%e f=%f  dp=%d\n",M,p,q,f,avg_dp);

    int i;

    for (i=0; i<call->n; i++)

    {
@@ -519,7 +519,7 @@ void calc_SegBias(const bcf_callret1_t *bcr, bcf_call_t *call) 
        else

            tmp = log(2*f*(1-f)*exp(-q) + f*f*exp(-2*q) + (1-f)*(1-f)) + p;

        sum += tmp;

        // fprintf(pysam_stderr,"oi=%d %e\n", oi,tmp);

        // fprintf(bcftools_stderr,"oi=%d %e\n", oi,tmp);

    }

    call->seg_bias = sum;

}
@@ -683,7 +683,7 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int 
            }

        }



//      if (ref_base < 0) fprintf(pysam_stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);

//      if (ref_base < 0) fprintf(bcftools_stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);

        call->shift = (int)(sum_min + .499);

    }

    // combine annotations