Package sam2indexedbam.sh with libhts.

scripts/sam2indexedbam.sh

+#!/usr/bin/env bash
+# Used to get mapping data suitable for making pileups or viewing with IGV
+# Usage: sam2indexedbam.sh <mapping.sam> [paired]
+# Add the option "paired" to only keep reads mapped in proper pair
+# Works if either <mapping.sam>, <mapping.sam.gz> or <mapping.sam.bz2> exists.
+# Generates two files: <mapping_sorted.bam> and <mapping_sorted.bam.bai>.
+
+# http://linuxcommand.org/wss0150.php
+PROGNAME=$(basename $0)
+
+tmpdir=$(mktemp -dt "${PROGNAME}.XXXXXXXXXX")
+
+cleanup()
+{
+    rm -rf ${tmpdir}
+}
+
+
+function error_exit
+{
+#	----------------------------------------------------------------
+#	Function for exit due to fatal program error
+#		Accepts 1 argument:
+#			string containing descriptive error message
+#	----------------------------------------------------------------
+    cleanup
+    echo "${PROGNAME}: ${1:-"Unknown Error"}" 1>&2
+    exit 1
+}
+
+samtools --version
+
+SAM=${1}
+
+case ${SAM} in
+    *.sam)
+        ext="sam"
+        ;;
+    *.bam)
+        ext="bam"
+        ;;
+    *)
+        error_exit "unrecognised file extension"
+        ;;
+esac
+
+# -F 4: skip reads that did not map
+if [[ ${2} ]]
+then
+    filter="-F 4 -f 2"
+else
+    filter="-F 4"
+fi
+
+# Test environment variable THREADS
+if [[ ${SAMTOOLS_THREADS} ]]
+then
+    threads_option="--threads ${SAMTOOLS_THREADS}"
+else
+    threads_option=""
+fi
+
+if [ -e ${SAM} ]
+then
+    # -u: output uncompressed bam, to save time when piping to samtools sort
+    samtools view ${threads_option} -u ${filter} ${SAM} | niceload --mem 500M samtools sort ${threads_option} -T ${tmpdir} -o ${SAM%.${ext}}_sorted.bam - || error_exit "samtools sort failed"
+    #cat ${SAM} | samtools view ${threads_option} -u ${filter} - | samtools sort ${threads_option} -o ${SAM%.${ext}}_sorted.bam - || error_exit "samtools sort failed"
+elif [ -e ${SAM}.gz ]
+then
+    zcat ${SAM}.gz | samtools view ${threads_option} -u ${filter} - | niceload --mem 500M samtools sort ${threads_option} -T ${tmpdir}  -o ${SAM%.${ext}}_sorted.bam - || error_exit "samtools sort failed"
+elif [ -e ${SAM}.bz2 ]
+then
+    bzcat ${SAM}.bz2 | samtools view ${threads_option} -u ${filter} - | niceload --mem 500M samtools sort ${threads_option} -T ${tmpdir}  -o ${SAM%.${ext}}_sorted.bam - || error_exit "samtools sort failed"
+else
+    echo "${SAM} not found, neither .gz or .bz2 versions."
+    echo "Aborting."
+    exit 1
+fi
+# There are random segmentation errors with samtools index
+#samtools index ${SAM%.sam}_sorted.bam || error_exit "samtools index failed"
+indexed=""
+while [ ! ${indexed} ]
+do
+    samtools index ${SAM%.${ext}}_sorted.bam && indexed="OK"
+    if [ ! ${indexed} ]
+    then
+        rm -f ${SAM%.${ext}}_sorted.bam.bai
+        echo "Indexing failed. Retrying" 1>&2
+    fi
+done || error_exit "samtools index failed"
+
+cleanup
+
+exit 0

setup.py

@@ -18,6 +18,7 @@ setup(
     author_email="blaise.li@normalesup.org",
     license="MIT",
     packages=find_packages(),
+    scripts=["scripts/sam2indexedbam.sh"],
     install_requires=[
         #"libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git@744dd79b579577cb6e131653260d7990946be3ad#egg=libworkflows-0.1",
         #"libworkflows @ git+https://gitlab+deploy-token-31:isEzpsgbNf2sJMdUDy2g@gitlab.pasteur.fr/bli/libworkflows.git#egg=libworkflows-0.1",