Workaround a bug with sam_parse1

Use old samtools to workaround a bug
teepean · Nov 8, 2019 · 89884ee · 89884ee
1 parent e111537
commit 89884ee
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Showing 3 changed files with 1 addition and 1 deletion.
diff --git a/BAM Analysis Kit.exe b/BAM Analysis Kit.exe
diff --git a/bin/cygwin/bin/samtoolsold.exe b/bin/cygwin/bin/samtoolsold.exe
diff --git a/console_bam.bat b/console_bam.bat
@@ -249,7 +249,7 @@ if "%%A" == "M" (
   DEL /Q /F inchr_tmp.sam
 )
 
-bin\cygwin\bin\bash.exe -c "bin/bow/samtools.exe view -@ %BAMKIT_THREADS% -bT ref.fa inchr.sam > reads.bam"
+bin\cygwin\bin\bash.exe -c "/bin/samtoolsold.exe view -bT ref.fa inchr.sam > reads.bam"
 bin\cygwin\bin\bash.exe -c "bin/bow/samtools.exe view -@ %BAMKIT_THREADS% -H inchr.bam|/bin/grep -v SN > header01"
 bin\cygwin\bin\bash.exe -c "bin/bow/samtools.exe view -@ %BAMKIT_THREADS% -H reads.bam > header02"
 copy header01+header02 header /Y /B > NUL