Commit 1452aced authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.8

parent d3c6ed11

.appveyor.yml

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# version format.

# you can use {branch} name in version format too

# version: 1.0.{build}-{branch}

version: 'vers.{build}'



# branches to build

branches:

    # Blacklist

    except:

      - gh-pages



# Do not build on tags (GitHub and BitBucket)

skip_tags: true



# Skipping commits affecting specific files (GitHub only). More details here: /docs/appveyor-yml

#skip_commits:

#  files:

#    - docs/*

#    - '**/*.html'



# We use Mingw/Msys, so use pacman for installs

install:

  - set HOME=.

  - set MSYSTEM=MINGW64

  - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%

  - set MINGWPREFIX=x86_64-w64-mingw32

  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\""



# The user may have e.g. jkbonfield/samtools branch FOO and an associated

# jkbonfield/htslib branch FOO.  If so use that related htslib, obtained by

# munging $APPVEYOR_REPO_NAME.  Otherwise we assume this is a PR only to

# samtools and should be linked against samtools(org)/htslib develop branch.

clone_script:

  - "sh -lc \"git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/$APPVEYOR_REPO_NAME $APPVEYOR_BUILD_FOLDER\""

  - "sh -lc \"git clone --branch=$APPVEYOR_REPO_BRANCH https://github.com/`echo $APPVEYOR_REPO_NAME|sed 's#/samtools#/htslib#'`.git $APPVEYOR_BUILD_FOLDER/htslib || git clone https://github.com/samtools/htslib.git $APPVEYOR_BUILD_FOLDER/htslib \""



build_script:

  - set HOME=.

  - set MSYSTEM=MINGW64

  - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%

  - "sh -lc \"(cd htslib; aclocal && autoheader && autoconf)\""

  - "sh -lc \"aclocal && autoheader && autoconf && ./configure && make -j2\""



test_script:

  - set HOME=.

  - set MSYSTEM=MINGW64

  - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%

  - "sh -lc \"make test\""

NEWS

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Release 1.8 (3rd April 2018)

----------------------------



 * samtools calmd now has a quiet mode.  This can be enabled by passing `-Q` to

   calmd. (Thanks to Colin Davenport)



 * In samtools depth `-d 0` will effectively remove the depth limit. (#764)



 * Improvements made to samtools collate's interface and documentation.  It is

   now possible to specify an output file name using `-o`, instead of deriving  

   it from the prefix used for temporary files.  The prefix itself is now

   optional if `-o` or `-O` (to stdout) is used. (#780)



 * Bug-fixes:



   - Make samtools addreplacerg choose output format by file extension. (#767; 

     reported by Argy Megalios)



   - Merge tests now work on ungzipped data, allowing tests to be run against

     different deflate libraries.



   - samtools markdup error messages about missing tags have been updated with

     the suggestion that samtools fixmate is run beforehand. (#765; reported by

     Yudong Cai)



   - Enables the `--reference` option for samtools fastq.  Now works like other

     programs when a reference sequence is needed for CRAM files. (#791,

     reported by Milana Kaljevic)





Release 1.7 (26th January 2018)

--------------------

README

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@@ -9,7 +9,7 @@ Building samtools 
The typical simple case of building Samtools using the HTSlib bundled within

this Samtools release tarball is done as follows:



    cd .../samtools-1.7 # Within the unpacked release directory

    cd .../samtools-1.8 # Within the unpacked release directory

    ./configure

    make
@@ -21,7 +21,7 @@ install samtools etc properly into a directory of your choosing. Building for 
installation using the HTSlib bundled within this Samtools release tarball,

and building the various HTSlib utilities such as bgzip is done as follows:



    cd .../samtools-1.7 # Within the unpacked release directory

    cd .../samtools-1.8 # Within the unpacked release directory

    ./configure --prefix=/path/to/location

    make all all-htslib

    make install install-htslib

bam.h

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@@ -38,7 +38,7 @@ DEALINGS IN THE SOFTWARE. */ 
  @copyright Genome Research Ltd.

 */



#define BAM_VERSION "1.7"

#define BAM_VERSION "1.8"



#include <stdint.h>

#include <stdlib.h>

bam2depth.c

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@@ -81,7 +81,8 @@ static int usage() { 
    fprintf(stderr, "   -b <bed>            list of positions or regions\n");

    fprintf(stderr, "   -f <list>           list of input BAM filenames, one per line [null]\n");

    fprintf(stderr, "   -l <int>            read length threshold (ignore reads shorter than <int>) [0]\n");

    fprintf(stderr, "   -d/-m <int>         maximum coverage depth [8000]\n");  // the htslib's default

    fprintf(stderr, "   -d/-m <int>         maximum coverage depth [8000]. If 0, depth is set to the maximum\n"

                    "                       integer value, effectively removing any depth limit.\n");  // the htslib's default

    fprintf(stderr, "   -q <int>            base quality threshold [0]\n");

    fprintf(stderr, "   -Q <int>            mapping quality threshold [0]\n");

    fprintf(stderr, "   -r <chr:from-to>    region\n");
@@ -206,6 +207,8 @@ int main_depth(int argc, char *argv[]) 
    mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization

    if (0 < max_depth)

        bam_mplp_set_maxcnt(mplp,max_depth);  // set maximum coverage depth

    else if (!max_depth)

        bam_mplp_set_maxcnt(mplp,INT_MAX);

    n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM

    plp = calloc(n, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads (internal in mplp)

    while ((ret=bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // come to the next covered position