7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/test/cross_validate.sh src/htslib/test/cross_validate.sh
deleted file mode 100755
index c8a531f2b92..00000000000
--- src/htslib/test/cross_validate.sh
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/bin/sh
-
-#
-# -----------------------------------------------------------------------------
-# Author: James Bonfield.
-#
-# This cross validation script is designed to run the htslib test_view
-# and cramtools.jar CRAM implementations to test compatibility between
-# implementations.  
-#
-# The test set may contain many dubious and ambiguous SAM cases, such as
-# single base reads (is that quality "*" really meaning Q9 or no quality?).
-# Some of these may fail one or the other implementations and be acceptable
-# in the short-term, so to spot more important regressions we can tag
-# specific cases as being known-pass or known-fail.
-# -----------------------------------------------------------------------------
-#
-
-vers=3.0
-
-cramtools_jar=$HOME/work/cram/cramtools/cramtools-$vers.jar
-
-test_view="./test_view -o VERSION=$vers"
-
-cramtools="/software/bin/java -Xmx4000m -jar $cramtools_jar"
-cramtools="/software/bin/java -Xmx4000m -jar $cramtools_jar"
-
-run_out() {
-    out=$1; shift
-    echo "$@ > $out"
-    $@ > $out
-}
-
-run() {
-    echo "$@"
-    $@
-}
-
-
-sam_to_Ccram() {
-    run_out _tmp.cram $test_view -C -t $1 $2
-    #run_out _tmp.cram $HOME/io_lib/trunk/build.seq3/progs/scramble -r $1 -O CRAM $2
-    if [ $? != 0 ]
-    then
-        crash=`expr $crash + 1`
-        false
-    fi
-}
-
-Ccram_to_sam() {
-    run_out _tmp.sam $test_view -i REFERENCE=$1 _tmp.cram
-    #run_out _tmp.sam $HOME/io_lib/trunk/build.seq3/progs/scramble -r $1 _tmp.cram
-
-    if [ $? != 0 ]
-    then
-        crash=`expr $crash + 1`
-        false
-    fi
-}
-
-sam_to_Jcram() {
-    run $cramtools cram -R $1 -I $2 -O _tmp.cram -n -Q --capture-all-tags
-    if [ $? != 0 ]
-    then
-        crash=`expr $crash + 1`
-        false
-    fi
-}
-
-Jcram_to_sam() {
-    run $cramtools bam -R $1 -I _tmp.cram -O _tmp.sam
-
-    if [ $? != 0 ]
-    then
-        crash=`expr $crash + 1`
-        false
-    fi
-}
-
-compare_sam() {
-    #run ./compare_sam.pl $i _tmp.sam -nomd -notemplate -unknownrg -Baux
-    run ./compare_sam.pl $i _tmp.sam -nomd -Baux
-    if [ $? != 0 ]
-    then
-        fails=`expr $fails + 1`
-        false
-    fi
-}
-
-trials=0
-fails=0
-crash=0
-
-files=`ls -1 *#*.sam`
-
-# Restrict to known workers from SAM->CRAM->CRAM in cramtools
-#files="auxf#values.sam c1#bounds.sam c1#noseq.sam c1#pad1.sam c1#pad2.sam c1#pad3.sam c1#unknown.sam ce#1.sam ce#2.sam ce#5b.sam ce#large_seq.sam ce#tag_depadded.sam ce#tag_padded.sam ce#unmap.sam ce#unmap1.sam ce#unmap2.sam xx#large_aux.sam xx#large_aux2.sam xx#pair.sam xx#rg.sam xx#unsorted.sam"
-
-for i in $files
-do
-    r=`echo $i | sed 's/#.*/.fa/'`
-    echo "=== $i"
-
-    # C to C
-    trials=`expr $trials + 1`
-    sam_to_Ccram $r $i && Ccram_to_sam $r && compare_sam $i _tmp.sam
-
-    # Java to Java
-    trials=`expr $trials + 1`
-    sam_to_Jcram $r $i && Jcram_to_sam $r && compare_sam $i _tmp.sam
-
-    # C to Java
-    trials=`expr $trials + 1`
-    sam_to_Ccram $r $i && Jcram_to_sam $r && compare_sam $i _tmp.sam
-    
-    # Java to C
-    trials=`expr $trials + 1`
-    sam_to_Jcram $r $i && Ccram_to_sam $r && compare_sam $i _tmp.sam
-done
-
-# Overcounts failures as an early fail can lead to 1 or 2 more fails.
-echo ""
-echo ============
-echo No. tests: $trials
-echo No. diffs: $fails
-echo No. crash: $crash